Starting phenix.real_space_refine on Sun Aug 9 09:11:12 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9sje_54945/08_2026/9sje_54945.cif Found real_map, /net/cci-nas-00/data/ceres_data/9sje_54945/08_2026/9sje_54945.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9sje_54945/08_2026/9sje_54945.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9sje_54945/08_2026/9sje_54945.map" model { file = "/net/cci-nas-00/data/ceres_data/9sje_54945/08_2026/9sje_54945.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9sje_54945/08_2026/9sje_54945.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 149 5.16 5 C 20733 2.51 5 N 5514 2.21 5 O 6522 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 32918 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 6987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 891, 6987 Classifications: {'peptide': 891} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 30, 'TRANS': 860} Chain: "B" Number of atoms: 3776 Number of conformers: 1 Conformer: "" Number of residues, atoms: 478, 3776 Classifications: {'peptide': 478} Link IDs: {'PTRANS': 21, 'TRANS': 456} Chain: "C" Number of atoms: 6890 Number of conformers: 1 Conformer: "" Number of residues, atoms: 878, 6890 Classifications: {'peptide': 878} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 30, 'TRANS': 847} Chain: "D" Number of atoms: 3776 Number of conformers: 1 Conformer: "" Number of residues, atoms: 478, 3776 Classifications: {'peptide': 478} Link IDs: {'PTRANS': 21, 'TRANS': 456} Chain: "E" Number of atoms: 1044 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1044 Classifications: {'peptide': 134} Link IDs: {'PTRANS': 1, 'TRANS': 132} Chain: "F" Number of atoms: 1044 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1044 Classifications: {'peptide': 134} Link IDs: {'PTRANS': 1, 'TRANS': 132} Chain: "G" Number of atoms: 4505 Number of conformers: 1 Conformer: "" Number of residues, atoms: 569, 4505 Classifications: {'peptide': 569} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 547} Chain: "H" Number of atoms: 4505 Number of conformers: 1 Conformer: "" Number of residues, atoms: 569, 4505 Classifications: {'peptide': 569} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 547} Chain: "I" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 45 Unusual residues: {'GLC': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "J" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 45 Unusual residues: {'GLC': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "K" Number of atoms: 89 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 89 Unusual residues: {'GLC': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "L" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 67 Unusual residues: {'GLC': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "M" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 78 Unusual residues: {'GLC': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "N" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 67 Unusual residues: {'GLC': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Time building chain proxies: 7.03, per 1000 atoms: 0.21 Number of scatterers: 32918 At special positions: 0 Unit cell: (152.904, 174.51, 177.003, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 149 16.00 O 6522 8.00 N 5514 7.00 C 20733 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-6 " GLC I 1 " - " GLC I 2 " " GLC I 2 " - " GLC I 3 " " GLC I 3 " - " GLC I 4 " " GLC J 1 " - " GLC J 2 " " GLC J 2 " - " GLC J 3 " " GLC J 3 " - " GLC J 4 " " GLC K 1 " - " GLC K 2 " " GLC K 2 " - " GLC K 3 " " GLC K 3 " - " GLC K 4 " " GLC K 4 " - " GLC K 5 " " GLC K 5 " - " GLC K 6 " " GLC K 6 " - " GLC K 7 " " GLC K 7 " - " GLC K 8 " " GLC L 1 " - " GLC L 2 " " GLC L 2 " - " GLC L 3 " " GLC L 3 " - " GLC L 4 " " GLC L 4 " - " GLC L 5 " " GLC L 5 " - " GLC L 6 " " GLC M 1 " - " GLC M 2 " " GLC M 2 " - " GLC M 3 " " GLC M 3 " - " GLC M 4 " " GLC M 4 " - " GLC M 5 " " GLC M 5 " - " GLC M 6 " " GLC M 6 " - " GLC M 7 " " GLC N 1 " - " GLC N 2 " " GLC N 2 " - " GLC N 3 " " GLC N 3 " - " GLC N 4 " " GLC N 4 " - " GLC N 5 " " GLC N 5 " - " GLC N 6 " Time building additional restraints: 2.96 Conformation dependent library (CDL) restraints added in 1.4 seconds 8230 Ramachandran restraints generated. 4115 Oldfield, 0 Emsley, 4115 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7602 Finding SS restraints... Secondary structure from input PDB file: 123 helices and 48 sheets defined 26.8% alpha, 28.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.04 Creating SS restraints... Processing helix chain 'A' and resid 135 through 137 No H-bonds generated for 'chain 'A' and resid 135 through 137' Processing helix chain 'A' and resid 144 through 149 Processing helix chain 'A' and resid 195 through 199 Processing helix chain 'A' and resid 200 through 202 No H-bonds generated for 'chain 'A' and resid 200 through 202' Processing helix chain 'A' and resid 212 through 217 Processing helix chain 'A' and resid 218 through 225 removed outlier: 6.608A pdb=" N SER A 221 " --> pdb=" O ILE A 218 " (cutoff:3.500A) removed outlier: 5.424A pdb=" N ALA A 224 " --> pdb=" O SER A 221 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N ASN A 225 " --> pdb=" O ARG A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 261 through 275 Processing helix chain 'A' and resid 281 through 285 Processing helix chain 'A' and resid 286 through 291 removed outlier: 3.821A pdb=" N GLY A 291 " --> pdb=" O SER A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 301 Processing helix chain 'A' and resid 376 through 383 Processing helix chain 'A' and resid 402 through 407 Processing helix chain 'A' and resid 413 through 419 Processing helix chain 'A' and resid 583 through 586 Processing helix chain 'A' and resid 600 through 603 Processing helix chain 'A' and resid 706 through 710 Processing helix chain 'A' and resid 799 through 806 Processing helix chain 'A' and resid 874 through 879 Processing helix chain 'A' and resid 888 through 894 Processing helix chain 'A' and resid 941 through 947 Processing helix chain 'B' and resid 38 through 49 removed outlier: 3.800A pdb=" N CYS B 49 " --> pdb=" O LEU B 45 " (cutoff:3.500A) Processing helix chain 'B' and resid 65 through 70 Processing helix chain 'B' and resid 83 through 91 Processing helix chain 'B' and resid 98 through 106 Processing helix chain 'B' and resid 107 through 122 Processing helix chain 'B' and resid 128 through 155 removed outlier: 3.814A pdb=" N ARG B 134 " --> pdb=" O GLU B 130 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ARG B 152 " --> pdb=" O TYR B 148 " (cutoff:3.500A) Processing helix chain 'B' and resid 176 through 195 removed outlier: 3.520A pdb=" N MET B 194 " --> pdb=" O ASN B 190 " (cutoff:3.500A) Processing helix chain 'B' and resid 197 through 201 Processing helix chain 'B' and resid 210 through 226 Processing helix chain 'B' and resid 227 through 230 removed outlier: 5.827A pdb=" N ARG B 230 " --> pdb=" O PRO B 227 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 227 through 230' Processing helix chain 'B' and resid 231 through 245 removed outlier: 3.900A pdb=" N GLU B 235 " --> pdb=" O ASP B 231 " (cutoff:3.500A) Processing helix chain 'B' and resid 254 through 259 Processing helix chain 'B' and resid 292 through 298 Processing helix chain 'B' and resid 317 through 322 removed outlier: 3.622A pdb=" N GLU B 321 " --> pdb=" O GLU B 317 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N TYR B 322 " --> pdb=" O PHE B 318 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 317 through 322' Processing helix chain 'B' and resid 327 through 332 removed outlier: 3.938A pdb=" N VAL B 331 " --> pdb=" O LEU B 327 " (cutoff:3.500A) Processing helix chain 'B' and resid 340 through 344 Processing helix chain 'B' and resid 347 through 351 Processing helix chain 'B' and resid 382 through 396 Processing helix chain 'B' and resid 399 through 401 No H-bonds generated for 'chain 'B' and resid 399 through 401' Processing helix chain 'B' and resid 402 through 411 removed outlier: 3.572A pdb=" N LEU B 406 " --> pdb=" O ALA B 402 " (cutoff:3.500A) Processing helix chain 'B' and resid 423 through 439 Processing helix chain 'B' and resid 443 through 452 removed outlier: 4.328A pdb=" N PHE B 447 " --> pdb=" O GLY B 443 " (cutoff:3.500A) Processing helix chain 'B' and resid 455 through 465 Processing helix chain 'B' and resid 480 through 485 Processing helix chain 'C' and resid 135 through 137 No H-bonds generated for 'chain 'C' and resid 135 through 137' Processing helix chain 'C' and resid 144 through 149 Processing helix chain 'C' and resid 195 through 199 Processing helix chain 'C' and resid 200 through 202 No H-bonds generated for 'chain 'C' and resid 200 through 202' Processing helix chain 'C' and resid 212 through 217 Processing helix chain 'C' and resid 218 through 220 No H-bonds generated for 'chain 'C' and resid 218 through 220' Processing helix chain 'C' and resid 222 through 225 removed outlier: 4.429A pdb=" N ASN C 225 " --> pdb=" O ARG C 222 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 222 through 225' Processing helix chain 'C' and resid 261 through 275 Processing helix chain 'C' and resid 281 through 285 Processing helix chain 'C' and resid 286 through 291 removed outlier: 3.965A pdb=" N GLY C 291 " --> pdb=" O SER C 288 " (cutoff:3.500A) Processing helix chain 'C' and resid 295 through 301 Processing helix chain 'C' and resid 376 through 381 Processing helix chain 'C' and resid 402 through 407 Processing helix chain 'C' and resid 413 through 419 removed outlier: 3.568A pdb=" N HIS C 417 " --> pdb=" O ILE C 413 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N MET C 419 " --> pdb=" O THR C 415 " (cutoff:3.500A) Processing helix chain 'C' and resid 534 through 538 Processing helix chain 'C' and resid 583 through 586 Processing helix chain 'C' and resid 600 through 603 Processing helix chain 'C' and resid 706 through 710 Processing helix chain 'C' and resid 799 through 806 Processing helix chain 'C' and resid 829 through 833 Processing helix chain 'C' and resid 874 through 879 Processing helix chain 'C' and resid 888 through 894 removed outlier: 3.502A pdb=" N ASN C 893 " --> pdb=" O ALA C 890 " (cutoff:3.500A) Processing helix chain 'C' and resid 941 through 947 Processing helix chain 'D' and resid 38 through 48 Processing helix chain 'D' and resid 49 through 51 No H-bonds generated for 'chain 'D' and resid 49 through 51' Processing helix chain 'D' and resid 65 through 70 removed outlier: 3.731A pdb=" N LEU D 69 " --> pdb=" O SER D 65 " (cutoff:3.500A) Processing helix chain 'D' and resid 83 through 91 Processing helix chain 'D' and resid 98 through 122 removed outlier: 4.216A pdb=" N SER D 107 " --> pdb=" O TYR D 103 " (cutoff:3.500A) Proline residue: D 108 - end of helix removed outlier: 3.658A pdb=" N ILE D 117 " --> pdb=" O GLY D 113 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N VAL D 118 " --> pdb=" O ARG D 114 " (cutoff:3.500A) Processing helix chain 'D' and resid 128 through 155 removed outlier: 3.912A pdb=" N ARG D 134 " --> pdb=" O GLU D 130 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ARG D 152 " --> pdb=" O TYR D 148 " (cutoff:3.500A) Processing helix chain 'D' and resid 176 through 195 Processing helix chain 'D' and resid 197 through 201 Processing helix chain 'D' and resid 210 through 226 Processing helix chain 'D' and resid 227 through 230 removed outlier: 5.424A pdb=" N ARG D 230 " --> pdb=" O PRO D 227 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 227 through 230' Processing helix chain 'D' and resid 231 through 245 removed outlier: 3.756A pdb=" N GLU D 235 " --> pdb=" O ASP D 231 " (cutoff:3.500A) Processing helix chain 'D' and resid 249 through 253 Processing helix chain 'D' and resid 255 through 259 Processing helix chain 'D' and resid 292 through 298 Processing helix chain 'D' and resid 315 through 320 Processing helix chain 'D' and resid 327 through 332 removed outlier: 4.178A pdb=" N VAL D 331 " --> pdb=" O LEU D 327 " (cutoff:3.500A) Processing helix chain 'D' and resid 347 through 351 Processing helix chain 'D' and resid 382 through 396 Processing helix chain 'D' and resid 398 through 414 removed outlier: 4.080A pdb=" N ALA D 404 " --> pdb=" O ASP D 400 " (cutoff:3.500A) Proline residue: D 405 - end of helix removed outlier: 3.571A pdb=" N ARG D 412 " --> pdb=" O ILE D 408 " (cutoff:3.500A) Processing helix chain 'D' and resid 423 through 439 removed outlier: 3.589A pdb=" N GLU D 429 " --> pdb=" O GLU D 425 " (cutoff:3.500A) Processing helix chain 'D' and resid 443 through 452 removed outlier: 4.368A pdb=" N PHE D 447 " --> pdb=" O GLY D 443 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ARG D 451 " --> pdb=" O PHE D 447 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ILE D 452 " --> pdb=" O ASP D 448 " (cutoff:3.500A) Processing helix chain 'D' and resid 455 through 466 Processing helix chain 'D' and resid 471 through 476 Processing helix chain 'D' and resid 480 through 487 Processing helix chain 'E' and resid 47 through 51 removed outlier: 4.131A pdb=" N ASN E 50 " --> pdb=" O ASN E 47 " (cutoff:3.500A) Processing helix chain 'E' and resid 104 through 114 Processing helix chain 'F' and resid 105 through 115 removed outlier: 3.833A pdb=" N GLN F 109 " --> pdb=" O GLU F 105 " (cutoff:3.500A) Processing helix chain 'G' and resid 148 through 162 Processing helix chain 'G' and resid 201 through 215 Processing helix chain 'G' and resid 237 through 241 Processing helix chain 'G' and resid 271 through 289 Processing helix chain 'G' and resid 314 through 330 Processing helix chain 'G' and resid 339 through 343 Processing helix chain 'G' and resid 344 through 350 Processing helix chain 'G' and resid 362 through 366 removed outlier: 3.887A pdb=" N ALA G 366 " --> pdb=" O ALA G 363 " (cutoff:3.500A) Processing helix chain 'G' and resid 367 through 382 removed outlier: 3.788A pdb=" N LEU G 371 " --> pdb=" O ASP G 367 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LYS G 372 " --> pdb=" O PHE G 368 " (cutoff:3.500A) Processing helix chain 'G' and resid 397 through 401 Processing helix chain 'G' and resid 406 through 420 Processing helix chain 'G' and resid 446 through 463 Processing helix chain 'G' and resid 463 through 468 Processing helix chain 'G' and resid 559 through 563 removed outlier: 3.883A pdb=" N GLY G 562 " --> pdb=" O VAL G 559 " (cutoff:3.500A) Processing helix chain 'H' and resid 148 through 162 Processing helix chain 'H' and resid 201 through 214 Processing helix chain 'H' and resid 230 through 235 removed outlier: 3.765A pdb=" N ASP H 234 " --> pdb=" O ASP H 230 " (cutoff:3.500A) Processing helix chain 'H' and resid 237 through 241 Processing helix chain 'H' and resid 271 through 289 Processing helix chain 'H' and resid 314 through 330 Processing helix chain 'H' and resid 339 through 343 Processing helix chain 'H' and resid 344 through 350 Processing helix chain 'H' and resid 362 through 366 removed outlier: 3.766A pdb=" N ALA H 366 " --> pdb=" O ALA H 363 " (cutoff:3.500A) Processing helix chain 'H' and resid 367 through 382 removed outlier: 3.550A pdb=" N LEU H 371 " --> pdb=" O ASP H 367 " (cutoff:3.500A) Processing helix chain 'H' and resid 397 through 401 Processing helix chain 'H' and resid 406 through 420 Processing helix chain 'H' and resid 446 through 463 removed outlier: 3.578A pdb=" N VAL H 454 " --> pdb=" O LYS H 450 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N HIS H 455 " --> pdb=" O THR H 451 " (cutoff:3.500A) Processing helix chain 'H' and resid 463 through 468 Processing helix chain 'H' and resid 559 through 563 Processing sheet with id=AA1, first strand: chain 'A' and resid 129 through 133 removed outlier: 6.704A pdb=" N LEU A 184 " --> pdb=" O VAL A 228 " (cutoff:3.500A) removed outlier: 7.754A pdb=" N ILE A 230 " --> pdb=" O LEU A 184 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N VAL A 186 " --> pdb=" O ILE A 230 " (cutoff:3.500A) removed outlier: 7.909A pdb=" N SER A 232 " --> pdb=" O VAL A 186 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N VAL A 185 " --> pdb=" O THR A 192 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 156 through 159 Processing sheet with id=AA3, first strand: chain 'A' and resid 964 through 966 removed outlier: 3.724A pdb=" N ASN A 952 " --> pdb=" O ASN A 998 " (cutoff:3.500A) removed outlier: 5.150A pdb=" N ALA A 239 " --> pdb=" O GLY A 316 " (cutoff:3.500A) removed outlier: 5.408A pdb=" N GLY A 316 " --> pdb=" O ALA A 239 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N VAL A 305 " --> pdb=" O SER A 332 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N LEU A 357 " --> pdb=" O VAL A 353 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLU A 422 " --> pdb=" O ASP A 458 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N SER A 543 " --> pdb=" O GLN A 523 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N ASN A 525 " --> pdb=" O MET A 541 " (cutoff:3.500A) removed outlier: 6.078A pdb=" N MET A 541 " --> pdb=" O ASN A 525 " (cutoff:3.500A) removed outlier: 10.811A pdb=" N THR A 590 " --> pdb=" O GLY A 626 " (cutoff:3.500A) removed outlier: 7.616A pdb=" N GLY A 626 " --> pdb=" O THR A 590 " (cutoff:3.500A) removed outlier: 5.062A pdb=" N GLY A 722 " --> pdb=" O ASP A 698 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N LEU A 700 " --> pdb=" O ASN A 720 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N ASN A 720 " --> pdb=" O LEU A 700 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N LYS A 702 " --> pdb=" O PHE A 718 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N PHE A 718 " --> pdb=" O LYS A 702 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N LYS A 723 " --> pdb=" O LEU A 758 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N TRP A 744 " --> pdb=" O ASN A 737 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N GLU A 857 " --> pdb=" O LEU A 936 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N LEU A 936 " --> pdb=" O GLU A 857 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N SER A 859 " --> pdb=" O ILE A 934 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N ILE A 934 " --> pdb=" O SER A 859 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N PHE A 861 " --> pdb=" O LYS A 932 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 639 through 640 Processing sheet with id=AA5, first strand: chain 'A' and resid 644 through 646 Processing sheet with id=AA6, first strand: chain 'A' and resid 766 through 771 removed outlier: 6.512A pdb=" N GLN A 770 " --> pdb=" O TYR A 775 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N TYR A 775 " --> pdb=" O GLN A 770 " (cutoff:3.500A) removed outlier: 5.395A pdb=" N VAL A 776 " --> pdb=" O TYR A 789 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N VAL A 787 " --> pdb=" O MET A 778 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N PHE A 788 " --> pdb=" O LEU A 836 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 793 through 796 removed outlier: 6.549A pdb=" N ARG A 818 " --> pdb=" O ASP A 794 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 923 through 925 removed outlier: 7.922A pdb=" N ASP A 981 " --> pdb=" O LYS A 869 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N TYR A 871 " --> pdb=" O ASP A 981 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 73 through 76 removed outlier: 6.202A pdb=" N GLY B 76 " --> pdb=" O TRP B 311 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N TRP B 311 " --> pdb=" O GLY B 76 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 269 through 273 removed outlier: 6.609A pdb=" N TYR B 380 " --> pdb=" O LEU B 270 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N GLU B 272 " --> pdb=" O VAL B 378 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N VAL B 378 " --> pdb=" O GLU B 272 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 333 through 334 Processing sheet with id=AB3, first strand: chain 'C' and resid 129 through 133 removed outlier: 4.053A pdb=" N VAL C 185 " --> pdb=" O THR C 192 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 156 through 159 Processing sheet with id=AB5, first strand: chain 'C' and resid 964 through 966 removed outlier: 3.532A pdb=" N ASN C 952 " --> pdb=" O ASN C 998 " (cutoff:3.500A) removed outlier: 5.298A pdb=" N ALA C 239 " --> pdb=" O GLY C 316 " (cutoff:3.500A) removed outlier: 5.309A pdb=" N GLY C 316 " --> pdb=" O ALA C 239 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N VAL C 305 " --> pdb=" O SER C 332 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N SER C 543 " --> pdb=" O GLN C 523 " (cutoff:3.500A) removed outlier: 5.915A pdb=" N ASN C 525 " --> pdb=" O MET C 541 " (cutoff:3.500A) removed outlier: 5.546A pdb=" N MET C 541 " --> pdb=" O ASN C 525 " (cutoff:3.500A) removed outlier: 10.117A pdb=" N THR C 590 " --> pdb=" O GLY C 626 " (cutoff:3.500A) removed outlier: 7.294A pdb=" N GLY C 626 " --> pdb=" O THR C 590 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N LYS C 723 " --> pdb=" O LEU C 758 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N TRP C 744 " --> pdb=" O ASN C 737 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N GLN C 863 " --> pdb=" O LEU C 931 " (cutoff:3.500A) removed outlier: 4.972A pdb=" N LEU C 931 " --> pdb=" O GLN C 863 " (cutoff:3.500A) removed outlier: 7.237A pdb=" N VAL C 865 " --> pdb=" O LEU C 929 " (cutoff:3.500A) removed outlier: 4.936A pdb=" N LEU C 929 " --> pdb=" O VAL C 865 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 643 through 644 Processing sheet with id=AB7, first strand: chain 'C' and resid 700 through 702 Processing sheet with id=AB8, first strand: chain 'C' and resid 766 through 771 removed outlier: 6.728A pdb=" N GLN C 770 " --> pdb=" O TYR C 775 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N TYR C 775 " --> pdb=" O GLN C 770 " (cutoff:3.500A) removed outlier: 5.257A pdb=" N VAL C 776 " --> pdb=" O TYR C 789 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N VAL C 787 " --> pdb=" O MET C 778 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N PHE C 788 " --> pdb=" O LEU C 836 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 793 through 796 removed outlier: 4.091A pdb=" N GLY C 795 " --> pdb=" O ARG C 818 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 923 through 925 removed outlier: 8.024A pdb=" N ASP C 981 " --> pdb=" O LYS C 869 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N TYR C 871 " --> pdb=" O ASP C 981 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 73 through 76 removed outlier: 6.370A pdb=" N GLY D 76 " --> pdb=" O TRP D 311 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N TRP D 311 " --> pdb=" O GLY D 76 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 269 through 273 removed outlier: 6.920A pdb=" N SER D 269 " --> pdb=" O ARG D 381 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N ARG D 381 " --> pdb=" O SER D 269 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N PHE D 271 " --> pdb=" O VAL D 379 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 333 through 334 Processing sheet with id=AC5, first strand: chain 'E' and resid 37 through 39 Processing sheet with id=AC6, first strand: chain 'E' and resid 43 through 46 Processing sheet with id=AC7, first strand: chain 'F' and resid 37 through 39 removed outlier: 3.556A pdb=" N LEU F 56 " --> pdb=" O LYS F 102 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'F' and resid 43 through 45 removed outlier: 6.745A pdb=" N ILE F 44 " --> pdb=" O THR F 150 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N GLN F 141 " --> pdb=" O ALA F 131 " (cutoff:3.500A) removed outlier: 8.177A pdb=" N ILE F 72 " --> pdb=" O THR F 95 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N THR F 95 " --> pdb=" O ILE F 72 " (cutoff:3.500A) removed outlier: 6.092A pdb=" N TYR F 74 " --> pdb=" O LEU F 93 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'G' and resid 39 through 41 removed outlier: 6.860A pdb=" N THR G 40 " --> pdb=" O ILE G 119 " (cutoff:3.500A) removed outlier: 8.007A pdb=" N GLY G 121 " --> pdb=" O THR G 40 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N LEU G 109 " --> pdb=" O VAL G 120 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N THR G 122 " --> pdb=" O ALA G 107 " (cutoff:3.500A) removed outlier: 7.223A pdb=" N ALA G 107 " --> pdb=" O THR G 122 " (cutoff:3.500A) removed outlier: 4.713A pdb=" N ALA G 124 " --> pdb=" O TYR G 105 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N TYR G 105 " --> pdb=" O ALA G 124 " (cutoff:3.500A) removed outlier: 4.910A pdb=" N ASP G 126 " --> pdb=" O LYS G 103 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N LYS G 103 " --> pdb=" O ASP G 126 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N VAL G 74 " --> pdb=" O GLU G 85 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N GLU G 85 " --> pdb=" O VAL G 74 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N TYR G 76 " --> pdb=" O VAL G 83 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'G' and resid 47 through 49 Processing sheet with id=AD2, first strand: chain 'G' and resid 137 through 140 removed outlier: 6.776A pdb=" N GLY G 138 " --> pdb=" O GLN G 168 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N SER G 218 " --> pdb=" O GLY G 293 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N GLN G 295 " --> pdb=" O SER G 218 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N PHE G 220 " --> pdb=" O GLN G 295 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N ALA G 297 " --> pdb=" O PHE G 220 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N ASN G 222 " --> pdb=" O ALA G 297 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'G' and resid 190 through 192 Processing sheet with id=AD4, first strand: chain 'G' and resid 226 through 227 Processing sheet with id=AD5, first strand: chain 'G' and resid 357 through 360 removed outlier: 6.487A pdb=" N PHE G 357 " --> pdb=" O VAL G 389 " (cutoff:3.500A) removed outlier: 7.649A pdb=" N ALA G 391 " --> pdb=" O PHE G 357 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N ASN G 359 " --> pdb=" O ALA G 391 " (cutoff:3.500A) removed outlier: 7.626A pdb=" N LEU G 425 " --> pdb=" O THR G 388 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N PHE G 390 " --> pdb=" O LEU G 425 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD5 Processing sheet with id=AD6, first strand: chain 'G' and resid 403 through 404 removed outlier: 6.746A pdb=" N GLY G 403 " --> pdb=" O THR G 444 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD6 Processing sheet with id=AD7, first strand: chain 'G' and resid 472 through 473 removed outlier: 7.211A pdb=" N ASN G 488 " --> pdb=" O THR G 499 " (cutoff:3.500A) removed outlier: 8.764A pdb=" N ALA G 501 " --> pdb=" O ASN G 488 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'G' and resid 472 through 473 Processing sheet with id=AD9, first strand: chain 'G' and resid 478 through 480 removed outlier: 6.628A pdb=" N THR G 540 " --> pdb=" O THR G 579 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N THR G 579 " --> pdb=" O THR G 540 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N GLN G 542 " --> pdb=" O SER G 577 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N SER G 577 " --> pdb=" O GLN G 542 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'H' and resid 39 through 41 removed outlier: 6.954A pdb=" N THR H 40 " --> pdb=" O ILE H 119 " (cutoff:3.500A) removed outlier: 7.705A pdb=" N GLY H 121 " --> pdb=" O THR H 40 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N LEU H 109 " --> pdb=" O VAL H 120 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N THR H 122 " --> pdb=" O ALA H 107 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N ALA H 107 " --> pdb=" O THR H 122 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N ALA H 124 " --> pdb=" O TYR H 105 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N TYR H 105 " --> pdb=" O ALA H 124 " (cutoff:3.500A) removed outlier: 4.928A pdb=" N ASP H 126 " --> pdb=" O LYS H 103 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N LYS H 103 " --> pdb=" O ASP H 126 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N GLY H 84 " --> pdb=" O TYR H 76 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N LEU H 78 " --> pdb=" O ILE H 82 " (cutoff:3.500A) removed outlier: 5.479A pdb=" N ILE H 82 " --> pdb=" O LEU H 78 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'H' and resid 47 through 49 Processing sheet with id=AE3, first strand: chain 'H' and resid 137 through 140 removed outlier: 6.816A pdb=" N SER H 218 " --> pdb=" O GLY H 293 " (cutoff:3.500A) removed outlier: 7.253A pdb=" N GLN H 295 " --> pdb=" O SER H 218 " (cutoff:3.500A) removed outlier: 6.028A pdb=" N PHE H 220 " --> pdb=" O GLN H 295 " (cutoff:3.500A) removed outlier: 7.356A pdb=" N ALA H 297 " --> pdb=" O PHE H 220 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N ASN H 222 " --> pdb=" O ALA H 297 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'H' and resid 182 through 183 Processing sheet with id=AE5, first strand: chain 'H' and resid 190 through 192 Processing sheet with id=AE6, first strand: chain 'H' and resid 226 through 227 Processing sheet with id=AE7, first strand: chain 'H' and resid 357 through 360 Processing sheet with id=AE8, first strand: chain 'H' and resid 403 through 404 removed outlier: 7.009A pdb=" N GLY H 403 " --> pdb=" O THR H 444 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE8 Processing sheet with id=AE9, first strand: chain 'H' and resid 472 through 474 removed outlier: 3.983A pdb=" N ALA H 501 " --> pdb=" O ASN H 474 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N ASN H 488 " --> pdb=" O THR H 499 " (cutoff:3.500A) removed outlier: 8.345A pdb=" N ALA H 501 " --> pdb=" O ASN H 488 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'H' and resid 472 through 474 removed outlier: 3.983A pdb=" N ALA H 501 " --> pdb=" O ASN H 474 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'H' and resid 478 through 480 Processing sheet with id=AF3, first strand: chain 'H' and resid 536 through 537 1468 hydrogen bonds defined for protein. 4005 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 8.36 Time building geometry restraints manager: 3.88 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 10623 1.34 - 1.46: 5767 1.46 - 1.57: 17028 1.57 - 1.69: 1 1.69 - 1.81: 266 Bond restraints: 33685 Sorted by residual: bond pdb=" C1 GLC M 2 " pdb=" O5 GLC M 2 " ideal model delta sigma weight residual 1.402 1.450 -0.048 2.00e-02 2.50e+03 5.79e+00 bond pdb=" CA LYS A 947 " pdb=" C LYS A 947 " ideal model delta sigma weight residual 1.520 1.509 0.011 4.80e-03 4.34e+04 5.33e+00 bond pdb=" C1 GLC N 1 " pdb=" O1 GLC N 1 " ideal model delta sigma weight residual 1.389 1.432 -0.043 2.00e-02 2.50e+03 4.60e+00 bond pdb=" C1 GLC L 1 " pdb=" O1 GLC L 1 " ideal model delta sigma weight residual 1.389 1.432 -0.043 2.00e-02 2.50e+03 4.59e+00 bond pdb=" C1 GLC M 2 " pdb=" C2 GLC M 2 " ideal model delta sigma weight residual 1.532 1.575 -0.043 2.00e-02 2.50e+03 4.55e+00 ... (remaining 33680 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.23: 44532 2.23 - 4.45: 1066 4.45 - 6.68: 125 6.68 - 8.91: 35 8.91 - 11.14: 4 Bond angle restraints: 45762 Sorted by residual: angle pdb=" N GLN C 949 " pdb=" CA GLN C 949 " pdb=" C GLN C 949 " ideal model delta sigma weight residual 114.64 107.38 7.26 1.52e+00 4.33e-01 2.28e+01 angle pdb=" C ARG B 106 " pdb=" N SER B 107 " pdb=" CA SER B 107 " ideal model delta sigma weight residual 121.80 132.94 -11.14 2.44e+00 1.68e-01 2.08e+01 angle pdb=" C ASN A 525 " pdb=" N ILE A 526 " pdb=" CA ILE A 526 " ideal model delta sigma weight residual 121.97 130.13 -8.16 1.80e+00 3.09e-01 2.05e+01 angle pdb=" C LEU C 760 " pdb=" N ASN C 761 " pdb=" CA ASN C 761 " ideal model delta sigma weight residual 121.54 129.40 -7.86 1.91e+00 2.74e-01 1.69e+01 angle pdb=" N SER D 107 " pdb=" CA SER D 107 " pdb=" C SER D 107 " ideal model delta sigma weight residual 109.81 118.59 -8.78 2.21e+00 2.05e-01 1.58e+01 ... (remaining 45757 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 18723 17.94 - 35.88: 1174 35.88 - 53.82: 235 53.82 - 71.77: 83 71.77 - 89.71: 31 Dihedral angle restraints: 20246 sinusoidal: 8310 harmonic: 11936 Sorted by residual: dihedral pdb=" CA SER A 651 " pdb=" C SER A 651 " pdb=" N THR A 652 " pdb=" CA THR A 652 " ideal model delta harmonic sigma weight residual -180.00 -151.89 -28.11 0 5.00e+00 4.00e-02 3.16e+01 dihedral pdb=" CA PHE G 390 " pdb=" C PHE G 390 " pdb=" N ALA G 391 " pdb=" CA ALA G 391 " ideal model delta harmonic sigma weight residual 180.00 151.92 28.08 0 5.00e+00 4.00e-02 3.15e+01 dihedral pdb=" CA GLU A 603 " pdb=" C GLU A 603 " pdb=" N ASP A 604 " pdb=" CA ASP A 604 " ideal model delta harmonic sigma weight residual 180.00 -152.45 -27.55 0 5.00e+00 4.00e-02 3.04e+01 ... (remaining 20243 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.074: 4270 0.074 - 0.147: 693 0.147 - 0.221: 50 0.221 - 0.295: 9 0.295 - 0.369: 6 Chirality restraints: 5028 Sorted by residual: chirality pdb=" C1 GLC L 3 " pdb=" O6 GLC L 2 " pdb=" C2 GLC L 3 " pdb=" O5 GLC L 3 " both_signs ideal model delta sigma weight residual False 2.40 2.15 0.25 2.00e-02 2.50e+03 1.62e+02 chirality pdb=" C1 GLC I 3 " pdb=" O6 GLC I 2 " pdb=" C2 GLC I 3 " pdb=" O5 GLC I 3 " both_signs ideal model delta sigma weight residual False 2.40 2.16 0.24 2.00e-02 2.50e+03 1.49e+02 chirality pdb=" C1 GLC M 2 " pdb=" O6 GLC M 1 " pdb=" C2 GLC M 2 " pdb=" O5 GLC M 2 " both_signs ideal model delta sigma weight residual False 2.40 2.16 0.24 2.00e-02 2.50e+03 1.44e+02 ... (remaining 5025 not shown) Planarity restraints: 5916 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG C 930 " 0.266 9.50e-02 1.11e+02 1.20e-01 1.11e+01 pdb=" NE ARG C 930 " -0.025 2.00e-02 2.50e+03 pdb=" CZ ARG C 930 " 0.023 2.00e-02 2.50e+03 pdb=" NH1 ARG C 930 " -0.011 2.00e-02 2.50e+03 pdb=" NH2 ARG C 930 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG H 136 " -0.252 9.50e-02 1.11e+02 1.14e-01 1.01e+01 pdb=" NE ARG H 136 " 0.024 2.00e-02 2.50e+03 pdb=" CZ ARG H 136 " -0.023 2.00e-02 2.50e+03 pdb=" NH1 ARG H 136 " 0.011 2.00e-02 2.50e+03 pdb=" NH2 ARG H 136 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 382 " -0.009 2.00e-02 2.50e+03 2.22e-02 9.82e+00 pdb=" CG TYR B 382 " 0.013 2.00e-02 2.50e+03 pdb=" CD1 TYR B 382 " -0.030 2.00e-02 2.50e+03 pdb=" CD2 TYR B 382 " 0.000 2.00e-02 2.50e+03 pdb=" CE1 TYR B 382 " 0.029 2.00e-02 2.50e+03 pdb=" CE2 TYR B 382 " -0.001 2.00e-02 2.50e+03 pdb=" CZ TYR B 382 " 0.030 2.00e-02 2.50e+03 pdb=" OH TYR B 382 " -0.032 2.00e-02 2.50e+03 ... (remaining 5913 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.79: 7421 2.79 - 3.32: 32135 3.32 - 3.85: 55462 3.85 - 4.37: 67456 4.37 - 4.90: 115766 Nonbonded interactions: 278240 Sorted by model distance: nonbonded pdb=" NH1 ARG G 184 " pdb=" OD1 ASP G 284 " model vdw 2.265 3.120 nonbonded pdb=" O PHE B 92 " pdb=" NH1 ARG B 474 " model vdw 2.266 3.120 nonbonded pdb=" O4 GLC M 3 " pdb=" O2 GLC M 5 " model vdw 2.286 3.040 nonbonded pdb=" NH1 ARG A 173 " pdb=" OE1 GLN A 671 " model vdw 2.294 3.120 nonbonded pdb=" OD1 ASP C 976 " pdb=" NH1 ARG C 984 " model vdw 2.294 3.120 ... (remaining 278235 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 122 through 999) selection = chain 'C' } ncs_group { reference = chain 'B' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' } ncs_group { reference = chain 'I' selection = chain 'J' } ncs_group { reference = (chain 'K' and resid 2 through 8) selection = (chain 'M' and (name C1 or name C2 or name C3 or name C4 or name C5 or name C6 o \ r name O2 or name O3 or name O4 or name O5 or name O6 )) } ncs_group { reference = chain 'L' selection = chain 'N' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.520 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 0.720 Check model and map are aligned: 0.100 Set scattering table: 0.060 Process input model: 31.900 Find NCS groups from input model: 0.560 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8764 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.152 33714 Z= 0.183 Angle : 0.864 31.922 45849 Z= 0.458 Chirality : 0.055 0.369 5028 Planarity : 0.007 0.120 5916 Dihedral : 13.491 89.708 12644 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 1.99 Ramachandran Plot: Outliers : 0.70 % Allowed : 4.50 % Favored : 94.80 % Rotamer: Outliers : 2.07 % Allowed : 5.86 % Favored : 92.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.19 (0.13), residues: 4115 helix: -1.21 (0.15), residues: 846 sheet: 1.04 (0.15), residues: 1147 loop : -0.23 (0.14), residues: 2122 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.027 0.004 ARG C 930 TYR 0.032 0.005 TYR B 382 PHE 0.028 0.002 PHE E 85 TRP 0.032 0.002 TRP F 100 HIS 0.008 0.001 HIS H 424 Details of bonding type rmsd/Z covalent geometry : bond 0.00380 / 0.18 (33685) covalent geometry : angle 0.83289 / 0.45 (45762) hydrogen bonds : bond 0.18234 / 12.33 ( 1463) hydrogen bonds : angle 7.74163 / 5.37 ( 4005) link_ALPHA1-6 : bond 0.02939 / 1.31 ( 29) link_ALPHA1-6 : angle 5.36524 / 3.58 ( 87) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8230 Ramachandran restraints generated. 4115 Oldfield, 0 Emsley, 4115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8230 Ramachandran restraints generated. 4115 Oldfield, 0 Emsley, 4115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 426 residues out of total 3483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 354 time to evaluate : 1.323 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 LYS cc_start: 0.7616 (mmtm) cc_final: 0.7207 (mmmm) REVERT: A 401 GLN cc_start: 0.8441 (tp-100) cc_final: 0.8203 (tp-100) REVERT: A 736 ILE cc_start: 0.9263 (pt) cc_final: 0.8889 (pp) REVERT: A 911 ASP cc_start: 0.8291 (t0) cc_final: 0.7576 (t70) REVERT: A 957 PHE cc_start: 0.8209 (m-80) cc_final: 0.8001 (m-10) REVERT: C 440 LYS cc_start: 0.9209 (mtpt) cc_final: 0.8999 (ttmt) REVERT: C 472 GLU cc_start: 0.8347 (OUTLIER) cc_final: 0.8056 (pm20) REVERT: C 690 ASP cc_start: 0.8795 (OUTLIER) cc_final: 0.8349 (t70) REVERT: C 741 ILE cc_start: 0.9243 (OUTLIER) cc_final: 0.9010 (pp) REVERT: C 948 ILE cc_start: 0.8170 (OUTLIER) cc_final: 0.7902 (mm) REVERT: D 282 ASP cc_start: 0.8521 (p0) cc_final: 0.8266 (p0) REVERT: F 42 GLN cc_start: 0.8351 (mm110) cc_final: 0.8121 (mm-40) REVERT: F 108 ASN cc_start: 0.8348 (m-40) cc_final: 0.8018 (m-40) REVERT: G 433 LEU cc_start: 0.9035 (OUTLIER) cc_final: 0.8831 (mm) REVERT: H 190 GLU cc_start: 0.8412 (OUTLIER) cc_final: 0.8039 (tm-30) REVERT: H 219 MET cc_start: 0.9119 (mmm) cc_final: 0.8260 (mmm) REVERT: H 394 MET cc_start: 0.8699 (mmm) cc_final: 0.8052 (mmt) outliers start: 72 outliers final: 19 residues processed: 418 average time/residue: 0.7000 time to fit residues: 349.6563 Evaluate side-chains 257 residues out of total 3483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 232 time to evaluate : 1.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 214 SER Chi-restraints excluded: chain A residue 600 VAL Chi-restraints excluded: chain A residue 773 ASN Chi-restraints excluded: chain A residue 836 LEU Chi-restraints excluded: chain A residue 943 LYS Chi-restraints excluded: chain B residue 401 GLN Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 472 GLU Chi-restraints excluded: chain C residue 676 VAL Chi-restraints excluded: chain C residue 690 ASP Chi-restraints excluded: chain C residue 741 ILE Chi-restraints excluded: chain C residue 776 VAL Chi-restraints excluded: chain C residue 787 VAL Chi-restraints excluded: chain C residue 836 LEU Chi-restraints excluded: chain C residue 948 ILE Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain F residue 50 ASN Chi-restraints excluded: chain G residue 225 PHE Chi-restraints excluded: chain G residue 433 LEU Chi-restraints excluded: chain H residue 68 LEU Chi-restraints excluded: chain H residue 190 GLU Chi-restraints excluded: chain H residue 404 GLU Chi-restraints excluded: chain H residue 580 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 197 optimal weight: 2.9990 chunk 388 optimal weight: 1.9990 chunk 215 optimal weight: 5.9990 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 0.0030 chunk 261 optimal weight: 7.9990 chunk 248 optimal weight: 0.9990 chunk 207 optimal weight: 2.9990 chunk 401 optimal weight: 10.0000 chunk 155 optimal weight: 10.0000 chunk 244 optimal weight: 0.8980 overall best weight: 1.3796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 157 GLN A 806 HIS A 946 GLN A 998 ASN B 175 ASN B 242 GLN B 411 GLN B 469 GLN C 469 ASN C 548 GLN C 809 GLN C 840 ASN C 998 ASN D 265 ASN D 274 GLN E 70 ASN E 108 ASN E 141 GLN G 338 ASN H 176 HIS H 263 ASN H 282 ASN H 288 ASN H 440 ASN ** H 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 544 ASN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.102258 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.065193 restraints weight = 68916.394| |-----------------------------------------------------------------------------| r_work (start): 0.3006 rms_B_bonded: 2.47 r_work: 0.2901 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2779 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.2779 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8920 moved from start: 0.1461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 33714 Z= 0.153 Angle : 0.674 10.464 45849 Z= 0.357 Chirality : 0.045 0.301 5028 Planarity : 0.004 0.054 5916 Dihedral : 6.665 73.477 5224 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.24 % Allowed : 3.35 % Favored : 96.40 % Rotamer: Outliers : 2.10 % Allowed : 9.96 % Favored : 87.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.43 (0.13), residues: 4115 helix: 0.35 (0.17), residues: 860 sheet: 0.88 (0.15), residues: 1136 loop : 0.03 (0.14), residues: 2119 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 445 TYR 0.028 0.002 TYR B 322 PHE 0.017 0.001 PHE E 85 TRP 0.019 0.001 TRP A 895 HIS 0.010 0.001 HIS B 398 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.15 (33685) covalent geometry : angle 0.66969 / 0.36 (45762) hydrogen bonds : bond 0.04256 / 2.90 ( 1463) hydrogen bonds : angle 5.57354 / 3.89 ( 4005) link_ALPHA1-6 : bond 0.00928 / 0.47 ( 29) link_ALPHA1-6 : angle 1.83852 / 1.23 ( 87) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8230 Ramachandran restraints generated. 4115 Oldfield, 0 Emsley, 4115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8230 Ramachandran restraints generated. 4115 Oldfield, 0 Emsley, 4115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 3483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 253 time to evaluate : 1.284 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 LYS cc_start: 0.7758 (mmtm) cc_final: 0.7311 (mmmm) REVERT: A 229 MET cc_start: 0.9127 (OUTLIER) cc_final: 0.8568 (mmm) REVERT: A 401 GLN cc_start: 0.8836 (tp-100) cc_final: 0.8477 (tp-100) REVERT: A 716 GLU cc_start: 0.7597 (OUTLIER) cc_final: 0.7312 (pm20) REVERT: A 957 PHE cc_start: 0.8384 (m-80) cc_final: 0.8087 (m-10) REVERT: B 398 HIS cc_start: 0.7342 (t70) cc_final: 0.6972 (t70) REVERT: B 401 GLN cc_start: 0.6953 (OUTLIER) cc_final: 0.6615 (pm20) REVERT: C 292 LYS cc_start: 0.9191 (OUTLIER) cc_final: 0.8841 (ttpt) REVERT: C 440 LYS cc_start: 0.9474 (mtpt) cc_final: 0.9267 (ttmt) REVERT: C 947 LYS cc_start: 0.7679 (OUTLIER) cc_final: 0.7050 (tppt) REVERT: C 951 GLU cc_start: 0.8375 (tm-30) cc_final: 0.8090 (pp20) REVERT: D 130 GLU cc_start: 0.8746 (pm20) cc_final: 0.8467 (pm20) REVERT: D 282 ASP cc_start: 0.8529 (p0) cc_final: 0.8267 (p0) REVERT: F 42 GLN cc_start: 0.8330 (mm110) cc_final: 0.8063 (tp-100) REVERT: F 103 LYS cc_start: 0.7616 (mmmm) cc_final: 0.7185 (mmmm) REVERT: F 108 ASN cc_start: 0.8544 (m-40) cc_final: 0.8247 (m110) REVERT: G 158 TYR cc_start: 0.8542 (t80) cc_final: 0.8277 (t80) REVERT: G 219 MET cc_start: 0.9042 (mmm) cc_final: 0.7400 (mmm) REVERT: G 326 MET cc_start: 0.8946 (OUTLIER) cc_final: 0.8328 (mpp) REVERT: G 433 LEU cc_start: 0.8563 (OUTLIER) cc_final: 0.8299 (mm) REVERT: G 463 TYR cc_start: 0.8598 (m-80) cc_final: 0.8283 (m-80) REVERT: H 33 VAL cc_start: 0.5073 (OUTLIER) cc_final: 0.4686 (p) REVERT: H 190 GLU cc_start: 0.8513 (OUTLIER) cc_final: 0.7977 (tm-30) REVERT: H 216 MET cc_start: 0.8564 (ptp) cc_final: 0.8178 (mtm) REVERT: H 219 MET cc_start: 0.8934 (mmm) cc_final: 0.7996 (mmm) REVERT: H 394 MET cc_start: 0.8361 (mmm) cc_final: 0.7212 (mmt) outliers start: 73 outliers final: 27 residues processed: 308 average time/residue: 0.6976 time to fit residues: 259.1247 Evaluate side-chains 260 residues out of total 3483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 224 time to evaluate : 1.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 131 SER Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 229 MET Chi-restraints excluded: chain A residue 600 VAL Chi-restraints excluded: chain A residue 624 VAL Chi-restraints excluded: chain A residue 716 GLU Chi-restraints excluded: chain A residue 836 LEU Chi-restraints excluded: chain A residue 943 LYS Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 401 GLN Chi-restraints excluded: chain C residue 199 LEU Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 292 LYS Chi-restraints excluded: chain C residue 472 GLU Chi-restraints excluded: chain C residue 585 ASN Chi-restraints excluded: chain C residue 676 VAL Chi-restraints excluded: chain C residue 690 ASP Chi-restraints excluded: chain C residue 836 LEU Chi-restraints excluded: chain C residue 947 LYS Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain E residue 33 ASP Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 124 SER Chi-restraints excluded: chain F residue 68 SER Chi-restraints excluded: chain F residue 117 VAL Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain G residue 326 MET Chi-restraints excluded: chain G residue 433 LEU Chi-restraints excluded: chain H residue 33 VAL Chi-restraints excluded: chain H residue 68 LEU Chi-restraints excluded: chain H residue 74 VAL Chi-restraints excluded: chain H residue 137 TYR Chi-restraints excluded: chain H residue 190 GLU Chi-restraints excluded: chain H residue 541 LEU Chi-restraints excluded: chain H residue 580 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 133 optimal weight: 10.0000 chunk 298 optimal weight: 20.0000 chunk 191 optimal weight: 5.9990 chunk 164 optimal weight: 3.9990 chunk 20 optimal weight: 3.9990 chunk 206 optimal weight: 7.9990 chunk 369 optimal weight: 10.0000 chunk 371 optimal weight: 10.0000 chunk 34 optimal weight: 0.9990 chunk 63 optimal weight: 3.9990 chunk 22 optimal weight: 0.9980 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 234 ASN B 375 ASN B 411 GLN C 649 ASN C 773 ASN ** F 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 338 ASN H 114 ASN H 282 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.100429 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.063213 restraints weight = 68721.043| |-----------------------------------------------------------------------------| r_work (start): 0.2968 rms_B_bonded: 2.44 r_work: 0.2862 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2741 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2741 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8979 moved from start: 0.1911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 33714 Z= 0.215 Angle : 0.639 10.204 45849 Z= 0.336 Chirality : 0.045 0.275 5028 Planarity : 0.004 0.065 5916 Dihedral : 6.158 65.600 5208 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.22 % Allowed : 3.96 % Favored : 95.82 % Rotamer: Outliers : 2.81 % Allowed : 10.94 % Favored : 86.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.41 (0.13), residues: 4115 helix: 0.67 (0.18), residues: 863 sheet: 0.63 (0.14), residues: 1188 loop : 0.00 (0.14), residues: 2064 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG E 128 TYR 0.025 0.002 TYR F 119 PHE 0.026 0.002 PHE E 85 TRP 0.019 0.001 TRP C 455 HIS 0.010 0.001 HIS F 51 Details of bonding type rmsd/Z covalent geometry : bond 0.00494 / 0.22 (33685) covalent geometry : angle 0.63409 / 0.34 (45762) hydrogen bonds : bond 0.03919 / 2.67 ( 1463) hydrogen bonds : angle 5.17688 / 3.60 ( 4005) link_ALPHA1-6 : bond 0.00857 / 0.45 ( 29) link_ALPHA1-6 : angle 1.86996 / 1.21 ( 87) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8230 Ramachandran restraints generated. 4115 Oldfield, 0 Emsley, 4115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8230 Ramachandran restraints generated. 4115 Oldfield, 0 Emsley, 4115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 3483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 239 time to evaluate : 1.219 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 LYS cc_start: 0.8164 (mmtm) cc_final: 0.7947 (mmmm) REVERT: A 234 ARG cc_start: 0.9145 (mtp85) cc_final: 0.8850 (mtm-85) REVERT: A 401 GLN cc_start: 0.8937 (tp-100) cc_final: 0.8584 (tp-100) REVERT: A 957 PHE cc_start: 0.8571 (m-80) cc_final: 0.8310 (m-10) REVERT: B 34 GLU cc_start: 0.8830 (OUTLIER) cc_final: 0.8561 (mt-10) REVERT: B 246 MET cc_start: 0.7797 (tpp) cc_final: 0.7385 (mtt) REVERT: B 262 THR cc_start: 0.8733 (t) cc_final: 0.8390 (p) REVERT: B 398 HIS cc_start: 0.7681 (t70) cc_final: 0.7412 (t70) REVERT: B 401 GLN cc_start: 0.6947 (OUTLIER) cc_final: 0.6674 (pm20) REVERT: C 234 ARG cc_start: 0.8352 (mtp-110) cc_final: 0.8090 (mtp-110) REVERT: C 292 LYS cc_start: 0.9211 (OUTLIER) cc_final: 0.8979 (ttpt) REVERT: C 350 ASP cc_start: 0.8084 (m-30) cc_final: 0.7763 (m-30) REVERT: C 741 ILE cc_start: 0.9309 (OUTLIER) cc_final: 0.9107 (pp) REVERT: C 947 LYS cc_start: 0.7739 (OUTLIER) cc_final: 0.7114 (tppt) REVERT: C 951 GLU cc_start: 0.8369 (tm-30) cc_final: 0.8064 (pp20) REVERT: D 61 GLN cc_start: 0.9405 (OUTLIER) cc_final: 0.8953 (tm-30) REVERT: D 130 GLU cc_start: 0.8727 (pm20) cc_final: 0.8440 (pm20) REVERT: D 282 ASP cc_start: 0.8591 (p0) cc_final: 0.8356 (p0) REVERT: E 142 ARG cc_start: 0.7943 (mtm180) cc_final: 0.7736 (mpp80) REVERT: F 24 ASP cc_start: 0.8544 (t0) cc_final: 0.8322 (t0) REVERT: F 51 HIS cc_start: 0.8521 (OUTLIER) cc_final: 0.7811 (p-80) REVERT: F 70 ASN cc_start: 0.9157 (m-40) cc_final: 0.8946 (m-40) REVERT: F 103 LYS cc_start: 0.7561 (mmmm) cc_final: 0.7276 (mmmm) REVERT: F 108 ASN cc_start: 0.8517 (m-40) cc_final: 0.7992 (m110) REVERT: F 110 PHE cc_start: 0.8671 (t80) cc_final: 0.8443 (t80) REVERT: F 119 TYR cc_start: 0.8379 (m-80) cc_final: 0.7753 (m-80) REVERT: F 122 LYS cc_start: 0.8781 (ttpp) cc_final: 0.8456 (tmtm) REVERT: G 219 MET cc_start: 0.9030 (mmm) cc_final: 0.7428 (mmm) REVERT: G 433 LEU cc_start: 0.8569 (OUTLIER) cc_final: 0.8262 (mm) REVERT: G 463 TYR cc_start: 0.8650 (m-80) cc_final: 0.8365 (m-80) REVERT: H 33 VAL cc_start: 0.4747 (OUTLIER) cc_final: 0.4357 (p) REVERT: H 190 GLU cc_start: 0.8528 (OUTLIER) cc_final: 0.7978 (tm-30) REVERT: H 219 MET cc_start: 0.8849 (mmm) cc_final: 0.7794 (mmm) REVERT: H 394 MET cc_start: 0.8289 (mmm) cc_final: 0.7183 (mmt) REVERT: H 485 MET cc_start: 0.7166 (OUTLIER) cc_final: 0.5947 (pmm) outliers start: 98 outliers final: 39 residues processed: 307 average time/residue: 0.6641 time to fit residues: 246.5112 Evaluate side-chains 271 residues out of total 3483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 221 time to evaluate : 1.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 131 SER Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 229 MET Chi-restraints excluded: chain A residue 600 VAL Chi-restraints excluded: chain A residue 624 VAL Chi-restraints excluded: chain A residue 735 THR Chi-restraints excluded: chain A residue 836 LEU Chi-restraints excluded: chain B residue 34 GLU Chi-restraints excluded: chain B residue 401 GLN Chi-restraints excluded: chain C residue 199 LEU Chi-restraints excluded: chain C residue 207 VAL Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 292 LYS Chi-restraints excluded: chain C residue 557 MET Chi-restraints excluded: chain C residue 585 ASN Chi-restraints excluded: chain C residue 612 LEU Chi-restraints excluded: chain C residue 641 THR Chi-restraints excluded: chain C residue 676 VAL Chi-restraints excluded: chain C residue 690 ASP Chi-restraints excluded: chain C residue 713 ASP Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 741 ILE Chi-restraints excluded: chain C residue 836 LEU Chi-restraints excluded: chain C residue 947 LYS Chi-restraints excluded: chain C residue 965 ILE Chi-restraints excluded: chain D residue 31 VAL Chi-restraints excluded: chain D residue 61 GLN Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain E residue 36 THR Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 52 THR Chi-restraints excluded: chain E residue 73 SER Chi-restraints excluded: chain E residue 124 SER Chi-restraints excluded: chain F residue 51 HIS Chi-restraints excluded: chain F residue 117 VAL Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain G residue 340 VAL Chi-restraints excluded: chain G residue 433 LEU Chi-restraints excluded: chain G residue 472 THR Chi-restraints excluded: chain G residue 509 VAL Chi-restraints excluded: chain H residue 33 VAL Chi-restraints excluded: chain H residue 37 THR Chi-restraints excluded: chain H residue 60 VAL Chi-restraints excluded: chain H residue 68 LEU Chi-restraints excluded: chain H residue 137 TYR Chi-restraints excluded: chain H residue 190 GLU Chi-restraints excluded: chain H residue 340 VAL Chi-restraints excluded: chain H residue 485 MET Chi-restraints excluded: chain H residue 541 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 398 optimal weight: 9.9990 chunk 158 optimal weight: 0.8980 chunk 47 optimal weight: 5.9990 chunk 150 optimal weight: 0.8980 chunk 191 optimal weight: 5.9990 chunk 19 optimal weight: 3.9990 chunk 302 optimal weight: 50.0000 chunk 267 optimal weight: 0.8980 chunk 91 optimal weight: 7.9990 chunk 197 optimal weight: 8.9990 chunk 225 optimal weight: 0.9980 overall best weight: 1.5382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 417 HIS A 673 ASN B 234 ASN B 264 ASN ** B 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 411 GLN F 42 GLN H 282 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.101610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.064904 restraints weight = 68467.038| |-----------------------------------------------------------------------------| r_work (start): 0.2991 rms_B_bonded: 2.48 r_work: 0.2883 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2762 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.2762 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8945 moved from start: 0.2144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 33714 Z= 0.141 Angle : 0.589 11.431 45849 Z= 0.308 Chirality : 0.043 0.254 5028 Planarity : 0.004 0.071 5916 Dihedral : 5.705 53.485 5199 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.62 % Favored : 96.21 % Rotamer: Outliers : 2.61 % Allowed : 11.94 % Favored : 85.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.43 (0.13), residues: 4115 helix: 0.86 (0.18), residues: 862 sheet: 0.62 (0.14), residues: 1180 loop : -0.06 (0.14), residues: 2073 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 445 TYR 0.017 0.001 TYR C 265 PHE 0.015 0.001 PHE F 110 TRP 0.019 0.001 TRP C 455 HIS 0.010 0.001 HIS B 398 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.14 (33685) covalent geometry : angle 0.58544 / 0.31 (45762) hydrogen bonds : bond 0.03377 / 2.31 ( 1463) hydrogen bonds : angle 4.93531 / 3.43 ( 4005) link_ALPHA1-6 : bond 0.00828 / 0.43 ( 29) link_ALPHA1-6 : angle 1.62960 / 1.07 ( 87) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8230 Ramachandran restraints generated. 4115 Oldfield, 0 Emsley, 4115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8230 Ramachandran restraints generated. 4115 Oldfield, 0 Emsley, 4115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 3483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 240 time to evaluate : 1.302 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 LYS cc_start: 0.8132 (mmtm) cc_final: 0.7804 (mmmm) REVERT: A 234 ARG cc_start: 0.9145 (mtp85) cc_final: 0.8850 (mtm-85) REVERT: A 401 GLN cc_start: 0.9021 (tp-100) cc_final: 0.8493 (tp40) REVERT: A 957 PHE cc_start: 0.8582 (m-80) cc_final: 0.8312 (m-10) REVERT: B 246 MET cc_start: 0.7795 (tpp) cc_final: 0.7320 (mtt) REVERT: B 262 THR cc_start: 0.8675 (t) cc_final: 0.8321 (p) REVERT: B 398 HIS cc_start: 0.7660 (t70) cc_final: 0.7458 (t70) REVERT: B 401 GLN cc_start: 0.6857 (OUTLIER) cc_final: 0.6540 (pm20) REVERT: C 234 ARG cc_start: 0.8311 (mtp-110) cc_final: 0.7970 (mtp-110) REVERT: C 292 LYS cc_start: 0.9213 (OUTLIER) cc_final: 0.9008 (ttpt) REVERT: C 350 ASP cc_start: 0.7977 (m-30) cc_final: 0.7611 (m-30) REVERT: C 419 MET cc_start: 0.9077 (OUTLIER) cc_final: 0.7815 (mpp) REVERT: C 947 LYS cc_start: 0.7711 (OUTLIER) cc_final: 0.7079 (tppt) REVERT: C 951 GLU cc_start: 0.8436 (tm-30) cc_final: 0.8119 (pp20) REVERT: D 61 GLN cc_start: 0.9343 (OUTLIER) cc_final: 0.8832 (tm-30) REVERT: D 422 LEU cc_start: 0.9036 (OUTLIER) cc_final: 0.8829 (tp) REVERT: E 29 ASP cc_start: 0.8687 (t70) cc_final: 0.8233 (t0) REVERT: F 39 VAL cc_start: 0.8669 (t) cc_final: 0.8412 (t) REVERT: F 51 HIS cc_start: 0.8516 (OUTLIER) cc_final: 0.7790 (p90) REVERT: F 70 ASN cc_start: 0.9156 (m-40) cc_final: 0.8890 (m-40) REVERT: F 103 LYS cc_start: 0.7608 (mmmm) cc_final: 0.7234 (mmmm) REVERT: F 108 ASN cc_start: 0.8295 (m-40) cc_final: 0.8086 (m110) REVERT: F 119 TYR cc_start: 0.8305 (m-80) cc_final: 0.7825 (m-80) REVERT: G 219 MET cc_start: 0.8948 (mmm) cc_final: 0.8653 (mmm) REVERT: G 326 MET cc_start: 0.8774 (OUTLIER) cc_final: 0.8374 (mpp) REVERT: G 433 LEU cc_start: 0.8501 (OUTLIER) cc_final: 0.8187 (mm) REVERT: G 463 TYR cc_start: 0.8681 (m-80) cc_final: 0.8374 (m-80) REVERT: H 33 VAL cc_start: 0.4507 (OUTLIER) cc_final: 0.4080 (p) REVERT: H 92 ASN cc_start: 0.8015 (OUTLIER) cc_final: 0.7516 (t0) REVERT: H 219 MET cc_start: 0.8819 (mmm) cc_final: 0.7668 (mmm) REVERT: H 394 MET cc_start: 0.8239 (mmm) cc_final: 0.7075 (mmt) outliers start: 91 outliers final: 41 residues processed: 308 average time/residue: 0.6410 time to fit residues: 241.2049 Evaluate side-chains 269 residues out of total 3483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 217 time to evaluate : 1.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 131 SER Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 600 VAL Chi-restraints excluded: chain A residue 624 VAL Chi-restraints excluded: chain A residue 836 LEU Chi-restraints excluded: chain A residue 945 LEU Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 401 GLN Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain C residue 207 VAL Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 292 LYS Chi-restraints excluded: chain C residue 329 LEU Chi-restraints excluded: chain C residue 419 MET Chi-restraints excluded: chain C residue 557 MET Chi-restraints excluded: chain C residue 612 LEU Chi-restraints excluded: chain C residue 685 VAL Chi-restraints excluded: chain C residue 690 ASP Chi-restraints excluded: chain C residue 751 THR Chi-restraints excluded: chain C residue 836 LEU Chi-restraints excluded: chain C residue 903 SER Chi-restraints excluded: chain C residue 947 LYS Chi-restraints excluded: chain C residue 965 ILE Chi-restraints excluded: chain D residue 58 MET Chi-restraints excluded: chain D residue 61 GLN Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain D residue 422 LEU Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 73 SER Chi-restraints excluded: chain E residue 129 ILE Chi-restraints excluded: chain E residue 142 ARG Chi-restraints excluded: chain F residue 50 ASN Chi-restraints excluded: chain F residue 51 HIS Chi-restraints excluded: chain F residue 117 VAL Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain G residue 326 MET Chi-restraints excluded: chain G residue 340 VAL Chi-restraints excluded: chain G residue 433 LEU Chi-restraints excluded: chain G residue 472 THR Chi-restraints excluded: chain G residue 478 MET Chi-restraints excluded: chain G residue 513 LEU Chi-restraints excluded: chain H residue 33 VAL Chi-restraints excluded: chain H residue 60 VAL Chi-restraints excluded: chain H residue 68 LEU Chi-restraints excluded: chain H residue 92 ASN Chi-restraints excluded: chain H residue 137 TYR Chi-restraints excluded: chain H residue 340 VAL Chi-restraints excluded: chain H residue 417 MET Chi-restraints excluded: chain H residue 541 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 381 optimal weight: 0.9990 chunk 361 optimal weight: 20.0000 chunk 110 optimal weight: 9.9990 chunk 250 optimal weight: 3.9990 chunk 368 optimal weight: 9.9990 chunk 316 optimal weight: 5.9990 chunk 38 optimal weight: 4.9990 chunk 30 optimal weight: 0.8980 chunk 380 optimal weight: 9.9990 chunk 169 optimal weight: 4.9990 chunk 9 optimal weight: 6.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 648 ASN ** B 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 330 HIS H 282 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.099834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.063816 restraints weight = 69092.509| |-----------------------------------------------------------------------------| r_work (start): 0.2961 rms_B_bonded: 2.44 r_work: 0.2844 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2724 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.2724 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8969 moved from start: 0.2285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 33714 Z= 0.235 Angle : 0.628 10.045 45849 Z= 0.326 Chirality : 0.044 0.321 5028 Planarity : 0.004 0.070 5916 Dihedral : 5.729 54.505 5195 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.16 % Favored : 95.67 % Rotamer: Outliers : 3.13 % Allowed : 12.09 % Favored : 84.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.32 (0.13), residues: 4115 helix: 0.81 (0.18), residues: 873 sheet: 0.53 (0.14), residues: 1187 loop : -0.15 (0.14), residues: 2055 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 142 TYR 0.026 0.002 TYR B 457 PHE 0.017 0.002 PHE F 110 TRP 0.017 0.001 TRP C 455 HIS 0.009 0.001 HIS B 398 Details of bonding type rmsd/Z covalent geometry : bond 0.00542 / 0.23 (33685) covalent geometry : angle 0.62363 / 0.33 (45762) hydrogen bonds : bond 0.03592 / 2.46 ( 1463) hydrogen bonds : angle 4.94372 / 3.44 ( 4005) link_ALPHA1-6 : bond 0.00873 / 0.47 ( 29) link_ALPHA1-6 : angle 1.72774 / 1.12 ( 87) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8230 Ramachandran restraints generated. 4115 Oldfield, 0 Emsley, 4115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8230 Ramachandran restraints generated. 4115 Oldfield, 0 Emsley, 4115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 3483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 221 time to evaluate : 1.366 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 234 ARG cc_start: 0.9156 (mtp85) cc_final: 0.8855 (mtm-85) REVERT: A 401 GLN cc_start: 0.9035 (tp-100) cc_final: 0.8742 (tp-100) REVERT: A 957 PHE cc_start: 0.8566 (m-80) cc_final: 0.8301 (m-10) REVERT: B 34 GLU cc_start: 0.8822 (OUTLIER) cc_final: 0.8579 (mt-10) REVERT: B 217 MET cc_start: 0.8487 (ttm) cc_final: 0.8088 (ttp) REVERT: B 246 MET cc_start: 0.7761 (tpp) cc_final: 0.7357 (mtt) REVERT: B 262 THR cc_start: 0.8792 (t) cc_final: 0.8448 (p) REVERT: B 398 HIS cc_start: 0.7691 (t70) cc_final: 0.7460 (t70) REVERT: B 401 GLN cc_start: 0.6659 (OUTLIER) cc_final: 0.6243 (pm20) REVERT: C 292 LYS cc_start: 0.9230 (OUTLIER) cc_final: 0.8967 (ttpt) REVERT: C 419 MET cc_start: 0.9092 (OUTLIER) cc_final: 0.7934 (mpp) REVERT: C 947 LYS cc_start: 0.7724 (OUTLIER) cc_final: 0.7068 (tppt) REVERT: D 61 GLN cc_start: 0.9399 (OUTLIER) cc_final: 0.8904 (tm-30) REVERT: D 422 LEU cc_start: 0.9053 (OUTLIER) cc_final: 0.8847 (tp) REVERT: F 39 VAL cc_start: 0.8641 (t) cc_final: 0.8374 (t) REVERT: F 51 HIS cc_start: 0.8520 (OUTLIER) cc_final: 0.7780 (p90) REVERT: F 70 ASN cc_start: 0.9214 (m-40) cc_final: 0.8961 (m-40) REVERT: F 103 LYS cc_start: 0.7653 (mmmm) cc_final: 0.7361 (mmmm) REVERT: F 108 ASN cc_start: 0.8306 (m-40) cc_final: 0.8033 (m110) REVERT: F 119 TYR cc_start: 0.8378 (m-80) cc_final: 0.7970 (m-80) REVERT: F 122 LYS cc_start: 0.8820 (ttpp) cc_final: 0.8478 (tmtm) REVERT: G 216 MET cc_start: 0.8074 (OUTLIER) cc_final: 0.7781 (mtt) REVERT: G 219 MET cc_start: 0.8906 (mmm) cc_final: 0.8606 (mmm) REVERT: G 326 MET cc_start: 0.8808 (OUTLIER) cc_final: 0.8374 (mpp) REVERT: G 433 LEU cc_start: 0.8511 (OUTLIER) cc_final: 0.8179 (mm) REVERT: G 463 TYR cc_start: 0.8675 (m-80) cc_final: 0.8361 (m-80) REVERT: H 92 ASN cc_start: 0.8054 (OUTLIER) cc_final: 0.7533 (t0) REVERT: H 219 MET cc_start: 0.8787 (mmm) cc_final: 0.7689 (mmm) REVERT: H 361 MET cc_start: 0.9040 (OUTLIER) cc_final: 0.8827 (mtp) REVERT: H 394 MET cc_start: 0.8238 (mmm) cc_final: 0.7062 (mmt) outliers start: 109 outliers final: 51 residues processed: 302 average time/residue: 0.6519 time to fit residues: 240.3938 Evaluate side-chains 278 residues out of total 3483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 214 time to evaluate : 1.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 131 SER Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 600 VAL Chi-restraints excluded: chain A residue 624 VAL Chi-restraints excluded: chain A residue 735 THR Chi-restraints excluded: chain A residue 836 LEU Chi-restraints excluded: chain A residue 965 ILE Chi-restraints excluded: chain B residue 34 GLU Chi-restraints excluded: chain B residue 128 SER Chi-restraints excluded: chain B residue 401 GLN Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain C residue 207 VAL Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 292 LYS Chi-restraints excluded: chain C residue 329 LEU Chi-restraints excluded: chain C residue 335 VAL Chi-restraints excluded: chain C residue 419 MET Chi-restraints excluded: chain C residue 557 MET Chi-restraints excluded: chain C residue 612 LEU Chi-restraints excluded: chain C residue 632 ASN Chi-restraints excluded: chain C residue 641 THR Chi-restraints excluded: chain C residue 685 VAL Chi-restraints excluded: chain C residue 690 ASP Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 751 THR Chi-restraints excluded: chain C residue 836 LEU Chi-restraints excluded: chain C residue 947 LYS Chi-restraints excluded: chain C residue 965 ILE Chi-restraints excluded: chain D residue 58 MET Chi-restraints excluded: chain D residue 61 GLN Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain D residue 422 LEU Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 73 SER Chi-restraints excluded: chain E residue 129 ILE Chi-restraints excluded: chain F residue 51 HIS Chi-restraints excluded: chain F residue 117 VAL Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain G residue 137 TYR Chi-restraints excluded: chain G residue 216 MET Chi-restraints excluded: chain G residue 326 MET Chi-restraints excluded: chain G residue 340 VAL Chi-restraints excluded: chain G residue 354 VAL Chi-restraints excluded: chain G residue 433 LEU Chi-restraints excluded: chain G residue 472 THR Chi-restraints excluded: chain G residue 509 VAL Chi-restraints excluded: chain G residue 513 LEU Chi-restraints excluded: chain G residue 549 VAL Chi-restraints excluded: chain H residue 37 THR Chi-restraints excluded: chain H residue 60 VAL Chi-restraints excluded: chain H residue 68 LEU Chi-restraints excluded: chain H residue 92 ASN Chi-restraints excluded: chain H residue 137 TYR Chi-restraints excluded: chain H residue 340 VAL Chi-restraints excluded: chain H residue 361 MET Chi-restraints excluded: chain H residue 417 MET Chi-restraints excluded: chain H residue 499 THR Chi-restraints excluded: chain H residue 509 VAL Chi-restraints excluded: chain H residue 541 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 26 optimal weight: 3.9990 chunk 340 optimal weight: 8.9990 chunk 213 optimal weight: 4.9990 chunk 373 optimal weight: 6.9990 chunk 40 optimal weight: 3.9990 chunk 282 optimal weight: 6.9990 chunk 73 optimal weight: 2.9990 chunk 235 optimal weight: 0.6980 chunk 210 optimal weight: 3.9990 chunk 363 optimal weight: 4.9990 chunk 155 optimal weight: 6.9990 overall best weight: 3.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 648 ASN B 234 ASN ** B 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 282 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.099675 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.063770 restraints weight = 68795.860| |-----------------------------------------------------------------------------| r_work (start): 0.2961 rms_B_bonded: 2.44 r_work: 0.2843 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2724 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.2724 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8974 moved from start: 0.2422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 33714 Z= 0.230 Angle : 0.624 12.261 45849 Z= 0.323 Chirality : 0.044 0.211 5028 Planarity : 0.004 0.069 5916 Dihedral : 5.785 56.380 5195 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.11 % Favored : 95.70 % Rotamer: Outliers : 3.10 % Allowed : 12.63 % Favored : 84.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.24 (0.13), residues: 4115 helix: 0.83 (0.18), residues: 873 sheet: 0.49 (0.14), residues: 1177 loop : -0.24 (0.14), residues: 2065 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 445 TYR 0.023 0.002 TYR B 322 PHE 0.013 0.001 PHE B 22 TRP 0.018 0.001 TRP C 455 HIS 0.008 0.001 HIS B 398 Details of bonding type rmsd/Z covalent geometry : bond 0.00529 / 0.23 (33685) covalent geometry : angle 0.62019 / 0.32 (45762) hydrogen bonds : bond 0.03511 / 2.40 ( 1463) hydrogen bonds : angle 4.89309 / 3.41 ( 4005) link_ALPHA1-6 : bond 0.00814 / 0.44 ( 29) link_ALPHA1-6 : angle 1.64140 / 1.07 ( 87) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8230 Ramachandran restraints generated. 4115 Oldfield, 0 Emsley, 4115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8230 Ramachandran restraints generated. 4115 Oldfield, 0 Emsley, 4115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 3483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 224 time to evaluate : 1.343 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 229 MET cc_start: 0.9030 (OUTLIER) cc_final: 0.8518 (mmm) REVERT: A 234 ARG cc_start: 0.9168 (mtp85) cc_final: 0.8873 (mtm-85) REVERT: A 318 GLU cc_start: 0.8554 (OUTLIER) cc_final: 0.7871 (tp30) REVERT: A 401 GLN cc_start: 0.9095 (tp-100) cc_final: 0.8824 (tp-100) REVERT: A 957 PHE cc_start: 0.8554 (m-80) cc_final: 0.8304 (m-10) REVERT: B 34 GLU cc_start: 0.8786 (OUTLIER) cc_final: 0.8571 (mt-10) REVERT: B 217 MET cc_start: 0.8467 (ttm) cc_final: 0.8067 (ttp) REVERT: B 246 MET cc_start: 0.7739 (tpp) cc_final: 0.7317 (mtt) REVERT: B 262 THR cc_start: 0.8882 (t) cc_final: 0.8558 (p) REVERT: C 419 MET cc_start: 0.9086 (OUTLIER) cc_final: 0.7912 (mpp) REVERT: C 947 LYS cc_start: 0.7690 (OUTLIER) cc_final: 0.7027 (tppt) REVERT: D 61 GLN cc_start: 0.9388 (OUTLIER) cc_final: 0.8882 (tm-30) REVERT: D 422 LEU cc_start: 0.9024 (OUTLIER) cc_final: 0.8807 (tp) REVERT: F 33 ASP cc_start: 0.8623 (t0) cc_final: 0.8402 (t0) REVERT: F 39 VAL cc_start: 0.8635 (t) cc_final: 0.8365 (t) REVERT: F 70 ASN cc_start: 0.9250 (m-40) cc_final: 0.8987 (m-40) REVERT: F 103 LYS cc_start: 0.7575 (mmmm) cc_final: 0.7303 (mmmm) REVERT: F 108 ASN cc_start: 0.8388 (m-40) cc_final: 0.8042 (m110) REVERT: F 122 LYS cc_start: 0.8799 (ttpp) cc_final: 0.8453 (tmtm) REVERT: G 216 MET cc_start: 0.8087 (OUTLIER) cc_final: 0.7748 (mtt) REVERT: G 219 MET cc_start: 0.8851 (mmm) cc_final: 0.8450 (mmm) REVERT: G 326 MET cc_start: 0.8796 (OUTLIER) cc_final: 0.8401 (mpp) REVERT: G 433 LEU cc_start: 0.8473 (OUTLIER) cc_final: 0.8126 (mm) REVERT: G 463 TYR cc_start: 0.8660 (m-80) cc_final: 0.8388 (m-80) REVERT: H 92 ASN cc_start: 0.8038 (OUTLIER) cc_final: 0.7537 (t0) REVERT: H 219 MET cc_start: 0.8740 (mmm) cc_final: 0.7642 (mmm) REVERT: H 361 MET cc_start: 0.9044 (OUTLIER) cc_final: 0.8841 (mtp) REVERT: H 394 MET cc_start: 0.8269 (mmm) cc_final: 0.7078 (mmt) outliers start: 108 outliers final: 50 residues processed: 306 average time/residue: 0.6360 time to fit residues: 237.7696 Evaluate side-chains 275 residues out of total 3483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 213 time to evaluate : 1.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 131 SER Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 229 MET Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain A residue 600 VAL Chi-restraints excluded: chain A residue 624 VAL Chi-restraints excluded: chain A residue 735 THR Chi-restraints excluded: chain A residue 836 LEU Chi-restraints excluded: chain A residue 965 ILE Chi-restraints excluded: chain B residue 34 GLU Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain C residue 207 VAL Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 272 MET Chi-restraints excluded: chain C residue 329 LEU Chi-restraints excluded: chain C residue 367 THR Chi-restraints excluded: chain C residue 419 MET Chi-restraints excluded: chain C residue 557 MET Chi-restraints excluded: chain C residue 612 LEU Chi-restraints excluded: chain C residue 632 ASN Chi-restraints excluded: chain C residue 641 THR Chi-restraints excluded: chain C residue 685 VAL Chi-restraints excluded: chain C residue 690 ASP Chi-restraints excluded: chain C residue 751 THR Chi-restraints excluded: chain C residue 836 LEU Chi-restraints excluded: chain C residue 947 LYS Chi-restraints excluded: chain C residue 965 ILE Chi-restraints excluded: chain D residue 58 MET Chi-restraints excluded: chain D residue 61 GLN Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain D residue 422 LEU Chi-restraints excluded: chain E residue 32 HIS Chi-restraints excluded: chain E residue 36 THR Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 73 SER Chi-restraints excluded: chain E residue 129 ILE Chi-restraints excluded: chain F residue 50 ASN Chi-restraints excluded: chain F residue 117 VAL Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain G residue 153 LEU Chi-restraints excluded: chain G residue 216 MET Chi-restraints excluded: chain G residue 326 MET Chi-restraints excluded: chain G residue 340 VAL Chi-restraints excluded: chain G residue 354 VAL Chi-restraints excluded: chain G residue 433 LEU Chi-restraints excluded: chain G residue 472 THR Chi-restraints excluded: chain G residue 513 LEU Chi-restraints excluded: chain H residue 37 THR Chi-restraints excluded: chain H residue 60 VAL Chi-restraints excluded: chain H residue 68 LEU Chi-restraints excluded: chain H residue 92 ASN Chi-restraints excluded: chain H residue 137 TYR Chi-restraints excluded: chain H residue 340 VAL Chi-restraints excluded: chain H residue 361 MET Chi-restraints excluded: chain H residue 417 MET Chi-restraints excluded: chain H residue 499 THR Chi-restraints excluded: chain H residue 509 VAL Chi-restraints excluded: chain H residue 541 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 292 optimal weight: 10.0000 chunk 15 optimal weight: 3.9990 chunk 301 optimal weight: 4.9990 chunk 142 optimal weight: 1.9990 chunk 241 optimal weight: 0.2980 chunk 91 optimal weight: 7.9990 chunk 279 optimal weight: 0.2980 chunk 303 optimal weight: 10.0000 chunk 48 optimal weight: 4.9990 chunk 358 optimal weight: 0.8980 chunk 234 optimal weight: 1.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 648 ASN A 863 GLN F 112 ASN H 288 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.101573 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.065057 restraints weight = 68543.948| |-----------------------------------------------------------------------------| r_work (start): 0.3000 rms_B_bonded: 2.46 r_work: 0.2887 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2766 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.2766 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8934 moved from start: 0.2585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 33714 Z= 0.118 Angle : 0.577 15.666 45849 Z= 0.298 Chirality : 0.042 0.361 5028 Planarity : 0.003 0.071 5916 Dihedral : 5.435 59.102 5192 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.77 % Favored : 96.06 % Rotamer: Outliers : 2.27 % Allowed : 13.75 % Favored : 83.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.36 (0.13), residues: 4115 helix: 0.99 (0.18), residues: 866 sheet: 0.54 (0.15), residues: 1166 loop : -0.17 (0.14), residues: 2083 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 142 TYR 0.026 0.001 TYR B 457 PHE 0.012 0.001 PHE F 110 TRP 0.020 0.001 TRP C 455 HIS 0.011 0.001 HIS F 51 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.12 (33685) covalent geometry : angle 0.57439 / 0.30 (45762) hydrogen bonds : bond 0.03051 / 2.08 ( 1463) hydrogen bonds : angle 4.71151 / 3.28 ( 4005) link_ALPHA1-6 : bond 0.00731 / 0.40 ( 29) link_ALPHA1-6 : angle 1.43782 / 0.94 ( 87) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8230 Ramachandran restraints generated. 4115 Oldfield, 0 Emsley, 4115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8230 Ramachandran restraints generated. 4115 Oldfield, 0 Emsley, 4115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 3483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 242 time to evaluate : 1.330 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 LYS cc_start: 0.8270 (mmtm) cc_final: 0.7996 (mmpt) REVERT: A 234 ARG cc_start: 0.9162 (mtp85) cc_final: 0.8856 (mtm-85) REVERT: A 518 ASP cc_start: 0.8877 (p0) cc_final: 0.8604 (p0) REVERT: A 957 PHE cc_start: 0.8533 (m-80) cc_final: 0.8263 (m-10) REVERT: B 194 MET cc_start: 0.8674 (ptt) cc_final: 0.8264 (ptp) REVERT: B 217 MET cc_start: 0.8447 (ttm) cc_final: 0.8065 (ttp) REVERT: B 246 MET cc_start: 0.7743 (tpp) cc_final: 0.7332 (OUTLIER) REVERT: B 262 THR cc_start: 0.8885 (t) cc_final: 0.8571 (p) REVERT: C 234 ARG cc_start: 0.8386 (OUTLIER) cc_final: 0.8091 (mtp-110) REVERT: C 419 MET cc_start: 0.9055 (OUTLIER) cc_final: 0.7783 (mpp) REVERT: C 690 ASP cc_start: 0.8957 (OUTLIER) cc_final: 0.8744 (m-30) REVERT: D 61 GLN cc_start: 0.9275 (OUTLIER) cc_final: 0.8754 (tm-30) REVERT: E 142 ARG cc_start: 0.7957 (mtm180) cc_final: 0.7533 (mpp80) REVERT: F 33 ASP cc_start: 0.8595 (t0) cc_final: 0.8342 (t0) REVERT: F 70 ASN cc_start: 0.9227 (m-40) cc_final: 0.8982 (m-40) REVERT: F 103 LYS cc_start: 0.7595 (mmmm) cc_final: 0.7347 (mmmm) REVERT: F 108 ASN cc_start: 0.8530 (m-40) cc_final: 0.8099 (m110) REVERT: F 122 LYS cc_start: 0.8868 (ttpp) cc_final: 0.8497 (tmtm) REVERT: G 219 MET cc_start: 0.8842 (mmm) cc_final: 0.8528 (mmm) REVERT: G 326 MET cc_start: 0.8725 (OUTLIER) cc_final: 0.8368 (mpp) REVERT: G 433 LEU cc_start: 0.8372 (OUTLIER) cc_final: 0.8070 (mm) REVERT: G 457 TYR cc_start: 0.8868 (m-80) cc_final: 0.8520 (m-80) REVERT: G 463 TYR cc_start: 0.8636 (m-80) cc_final: 0.8336 (m-80) REVERT: H 92 ASN cc_start: 0.8079 (OUTLIER) cc_final: 0.7593 (t0) REVERT: H 156 MET cc_start: 0.9106 (mmm) cc_final: 0.8190 (mmm) REVERT: H 219 MET cc_start: 0.8717 (mmm) cc_final: 0.7596 (mmm) REVERT: H 394 MET cc_start: 0.8249 (mmm) cc_final: 0.7059 (mmt) outliers start: 79 outliers final: 44 residues processed: 300 average time/residue: 0.6207 time to fit residues: 227.5863 Evaluate side-chains 270 residues out of total 3483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 220 time to evaluate : 1.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 131 SER Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 624 VAL Chi-restraints excluded: chain A residue 836 LEU Chi-restraints excluded: chain B residue 128 SER Chi-restraints excluded: chain C residue 234 ARG Chi-restraints excluded: chain C residue 272 MET Chi-restraints excluded: chain C residue 329 LEU Chi-restraints excluded: chain C residue 335 VAL Chi-restraints excluded: chain C residue 367 THR Chi-restraints excluded: chain C residue 419 MET Chi-restraints excluded: chain C residue 487 LEU Chi-restraints excluded: chain C residue 557 MET Chi-restraints excluded: chain C residue 612 LEU Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 632 ASN Chi-restraints excluded: chain C residue 641 THR Chi-restraints excluded: chain C residue 690 ASP Chi-restraints excluded: chain C residue 751 THR Chi-restraints excluded: chain C residue 787 VAL Chi-restraints excluded: chain C residue 836 LEU Chi-restraints excluded: chain C residue 965 ILE Chi-restraints excluded: chain D residue 32 ASP Chi-restraints excluded: chain D residue 61 GLN Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain E residue 32 HIS Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 73 SER Chi-restraints excluded: chain E residue 129 ILE Chi-restraints excluded: chain F residue 117 VAL Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain G residue 326 MET Chi-restraints excluded: chain G residue 340 VAL Chi-restraints excluded: chain G residue 433 LEU Chi-restraints excluded: chain G residue 478 MET Chi-restraints excluded: chain G residue 509 VAL Chi-restraints excluded: chain G residue 513 LEU Chi-restraints excluded: chain H residue 37 THR Chi-restraints excluded: chain H residue 60 VAL Chi-restraints excluded: chain H residue 68 LEU Chi-restraints excluded: chain H residue 92 ASN Chi-restraints excluded: chain H residue 137 TYR Chi-restraints excluded: chain H residue 340 VAL Chi-restraints excluded: chain H residue 417 MET Chi-restraints excluded: chain H residue 499 THR Chi-restraints excluded: chain H residue 509 VAL Chi-restraints excluded: chain H residue 541 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 93 optimal weight: 6.9990 chunk 172 optimal weight: 0.9980 chunk 66 optimal weight: 6.9990 chunk 57 optimal weight: 3.9990 chunk 39 optimal weight: 8.9990 chunk 337 optimal weight: 1.9990 chunk 254 optimal weight: 0.9990 chunk 407 optimal weight: 5.9990 chunk 167 optimal weight: 7.9990 chunk 273 optimal weight: 10.0000 chunk 305 optimal weight: 9.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 648 ASN B 234 ASN ** B 398 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.099896 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.063408 restraints weight = 68819.183| |-----------------------------------------------------------------------------| r_work (start): 0.2965 rms_B_bonded: 2.54 r_work: 0.2844 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2722 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2722 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8968 moved from start: 0.2613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 33714 Z= 0.212 Angle : 0.616 15.440 45849 Z= 0.318 Chirality : 0.044 0.321 5028 Planarity : 0.004 0.069 5916 Dihedral : 5.493 57.497 5190 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.11 % Favored : 95.70 % Rotamer: Outliers : 2.33 % Allowed : 14.24 % Favored : 83.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.31 (0.13), residues: 4115 helix: 1.00 (0.18), residues: 862 sheet: 0.49 (0.15), residues: 1148 loop : -0.21 (0.14), residues: 2105 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 128 TYR 0.041 0.001 TYR E 119 PHE 0.018 0.001 PHE F 85 TRP 0.024 0.001 TRP H 274 HIS 0.011 0.001 HIS F 51 Details of bonding type rmsd/Z covalent geometry : bond 0.00486 / 0.21 (33685) covalent geometry : angle 0.61274 / 0.32 (45762) hydrogen bonds : bond 0.03345 / 2.29 ( 1463) hydrogen bonds : angle 4.77072 / 3.32 ( 4005) link_ALPHA1-6 : bond 0.00802 / 0.44 ( 29) link_ALPHA1-6 : angle 1.59558 / 1.04 ( 87) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8230 Ramachandran restraints generated. 4115 Oldfield, 0 Emsley, 4115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8230 Ramachandran restraints generated. 4115 Oldfield, 0 Emsley, 4115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 3483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 220 time to evaluate : 1.088 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 LYS cc_start: 0.8269 (mmtm) cc_final: 0.8004 (mmpt) REVERT: A 234 ARG cc_start: 0.9184 (mtp85) cc_final: 0.8876 (mtm-85) REVERT: A 401 GLN cc_start: 0.9180 (tp40) cc_final: 0.8715 (tp40) REVERT: A 957 PHE cc_start: 0.8553 (m-80) cc_final: 0.8295 (m-10) REVERT: B 217 MET cc_start: 0.8436 (ttm) cc_final: 0.8044 (ttp) REVERT: B 246 MET cc_start: 0.7760 (tpp) cc_final: 0.7363 (OUTLIER) REVERT: B 262 THR cc_start: 0.8926 (t) cc_final: 0.8608 (p) REVERT: B 398 HIS cc_start: 0.7183 (t70) cc_final: 0.6982 (t70) REVERT: C 419 MET cc_start: 0.9083 (OUTLIER) cc_final: 0.7911 (mpp) REVERT: D 61 GLN cc_start: 0.9390 (OUTLIER) cc_final: 0.8875 (tm-30) REVERT: F 33 ASP cc_start: 0.8684 (t0) cc_final: 0.8437 (t0) REVERT: F 70 ASN cc_start: 0.9255 (m-40) cc_final: 0.8983 (m-40) REVERT: F 103 LYS cc_start: 0.7593 (mmmm) cc_final: 0.7307 (mmmm) REVERT: F 122 LYS cc_start: 0.8864 (ttpp) cc_final: 0.8488 (tmtm) REVERT: G 219 MET cc_start: 0.8853 (mmm) cc_final: 0.8545 (mmm) REVERT: G 326 MET cc_start: 0.8755 (OUTLIER) cc_final: 0.8412 (mpp) REVERT: G 394 MET cc_start: 0.8667 (OUTLIER) cc_final: 0.8068 (mtp) REVERT: G 433 LEU cc_start: 0.8415 (OUTLIER) cc_final: 0.8053 (mm) REVERT: G 463 TYR cc_start: 0.8662 (m-80) cc_final: 0.8326 (m-80) REVERT: H 92 ASN cc_start: 0.8124 (OUTLIER) cc_final: 0.7557 (t0) REVERT: H 219 MET cc_start: 0.8723 (mmm) cc_final: 0.7592 (mmm) REVERT: H 394 MET cc_start: 0.8221 (mmm) cc_final: 0.7006 (mmt) outliers start: 81 outliers final: 51 residues processed: 281 average time/residue: 0.5918 time to fit residues: 204.1057 Evaluate side-chains 270 residues out of total 3483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 214 time to evaluate : 1.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 131 SER Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 474 SER Chi-restraints excluded: chain A residue 487 LEU Chi-restraints excluded: chain A residue 624 VAL Chi-restraints excluded: chain A residue 735 THR Chi-restraints excluded: chain A residue 836 LEU Chi-restraints excluded: chain B residue 128 SER Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain C residue 207 VAL Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 272 MET Chi-restraints excluded: chain C residue 329 LEU Chi-restraints excluded: chain C residue 367 THR Chi-restraints excluded: chain C residue 419 MET Chi-restraints excluded: chain C residue 557 MET Chi-restraints excluded: chain C residue 612 LEU Chi-restraints excluded: chain C residue 632 ASN Chi-restraints excluded: chain C residue 641 THR Chi-restraints excluded: chain C residue 685 VAL Chi-restraints excluded: chain C residue 690 ASP Chi-restraints excluded: chain C residue 751 THR Chi-restraints excluded: chain C residue 836 LEU Chi-restraints excluded: chain C residue 965 ILE Chi-restraints excluded: chain D residue 61 GLN Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain D residue 400 ASP Chi-restraints excluded: chain E residue 32 HIS Chi-restraints excluded: chain E residue 36 THR Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 129 ILE Chi-restraints excluded: chain F residue 117 VAL Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain G residue 326 MET Chi-restraints excluded: chain G residue 340 VAL Chi-restraints excluded: chain G residue 354 VAL Chi-restraints excluded: chain G residue 394 MET Chi-restraints excluded: chain G residue 433 LEU Chi-restraints excluded: chain G residue 472 THR Chi-restraints excluded: chain G residue 478 MET Chi-restraints excluded: chain G residue 509 VAL Chi-restraints excluded: chain G residue 513 LEU Chi-restraints excluded: chain G residue 549 VAL Chi-restraints excluded: chain H residue 37 THR Chi-restraints excluded: chain H residue 60 VAL Chi-restraints excluded: chain H residue 68 LEU Chi-restraints excluded: chain H residue 92 ASN Chi-restraints excluded: chain H residue 137 TYR Chi-restraints excluded: chain H residue 340 VAL Chi-restraints excluded: chain H residue 417 MET Chi-restraints excluded: chain H residue 499 THR Chi-restraints excluded: chain H residue 509 VAL Chi-restraints excluded: chain H residue 541 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 12 optimal weight: 1.9990 chunk 321 optimal weight: 10.0000 chunk 108 optimal weight: 9.9990 chunk 8 optimal weight: 0.6980 chunk 276 optimal weight: 9.9990 chunk 404 optimal weight: 7.9990 chunk 385 optimal weight: 6.9990 chunk 228 optimal weight: 0.4980 chunk 291 optimal weight: 9.9990 chunk 325 optimal weight: 4.9990 chunk 332 optimal weight: 5.9990 overall best weight: 2.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 648 ASN F 112 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.099788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.063384 restraints weight = 68536.577| |-----------------------------------------------------------------------------| r_work (start): 0.2962 rms_B_bonded: 2.54 r_work: 0.2837 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2715 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.2715 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9008 moved from start: 0.2672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 33714 Z= 0.213 Angle : 0.613 15.536 45849 Z= 0.317 Chirality : 0.044 0.307 5028 Planarity : 0.004 0.069 5916 Dihedral : 5.558 56.060 5190 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.30 % Favored : 95.50 % Rotamer: Outliers : 2.15 % Allowed : 14.56 % Favored : 83.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.26 (0.13), residues: 4115 helix: 1.00 (0.18), residues: 860 sheet: 0.43 (0.15), residues: 1154 loop : -0.25 (0.14), residues: 2101 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 142 TYR 0.025 0.001 TYR B 457 PHE 0.015 0.001 PHE F 110 TRP 0.025 0.001 TRP H 274 HIS 0.013 0.001 HIS F 51 Details of bonding type rmsd/Z covalent geometry : bond 0.00489 / 0.21 (33685) covalent geometry : angle 0.60941 / 0.32 (45762) hydrogen bonds : bond 0.03347 / 2.28 ( 1463) hydrogen bonds : angle 4.78101 / 3.33 ( 4005) link_ALPHA1-6 : bond 0.00805 / 0.44 ( 29) link_ALPHA1-6 : angle 1.56876 / 1.03 ( 87) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8230 Ramachandran restraints generated. 4115 Oldfield, 0 Emsley, 4115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8230 Ramachandran restraints generated. 4115 Oldfield, 0 Emsley, 4115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 3483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 219 time to evaluate : 1.254 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 LYS cc_start: 0.8306 (mmtm) cc_final: 0.8084 (mmpt) REVERT: A 234 ARG cc_start: 0.9188 (mtp85) cc_final: 0.8900 (mtm-85) REVERT: A 401 GLN cc_start: 0.9220 (tp40) cc_final: 0.8814 (tp40) REVERT: A 957 PHE cc_start: 0.8567 (m-80) cc_final: 0.8316 (m-10) REVERT: B 217 MET cc_start: 0.8474 (ttm) cc_final: 0.8066 (ttp) REVERT: B 246 MET cc_start: 0.7764 (tpp) cc_final: 0.7391 (OUTLIER) REVERT: C 234 ARG cc_start: 0.8452 (OUTLIER) cc_final: 0.8212 (mtp-110) REVERT: C 419 MET cc_start: 0.9098 (OUTLIER) cc_final: 0.7885 (mpp) REVERT: D 61 GLN cc_start: 0.9365 (OUTLIER) cc_final: 0.8863 (tm-30) REVERT: F 33 ASP cc_start: 0.8772 (t0) cc_final: 0.8492 (t0) REVERT: F 53 GLN cc_start: 0.9328 (pm20) cc_final: 0.9118 (pm20) REVERT: F 70 ASN cc_start: 0.9266 (m-40) cc_final: 0.9003 (m-40) REVERT: F 103 LYS cc_start: 0.7664 (mmmm) cc_final: 0.7386 (mmmm) REVERT: F 122 LYS cc_start: 0.8875 (ttpp) cc_final: 0.8484 (tmtm) REVERT: G 219 MET cc_start: 0.8854 (mmm) cc_final: 0.8542 (mmm) REVERT: G 326 MET cc_start: 0.8779 (OUTLIER) cc_final: 0.8447 (mpp) REVERT: G 394 MET cc_start: 0.8652 (OUTLIER) cc_final: 0.8044 (mtp) REVERT: G 433 LEU cc_start: 0.8406 (OUTLIER) cc_final: 0.8068 (mm) REVERT: G 457 TYR cc_start: 0.8938 (m-80) cc_final: 0.8605 (m-80) REVERT: G 463 TYR cc_start: 0.8661 (m-80) cc_final: 0.8317 (m-80) REVERT: H 92 ASN cc_start: 0.8136 (OUTLIER) cc_final: 0.7575 (t0) REVERT: H 156 MET cc_start: 0.9131 (mmm) cc_final: 0.8212 (mmm) REVERT: H 219 MET cc_start: 0.8709 (mmm) cc_final: 0.7583 (mmm) REVERT: H 394 MET cc_start: 0.8249 (mmm) cc_final: 0.7038 (mmt) outliers start: 75 outliers final: 53 residues processed: 275 average time/residue: 0.6158 time to fit residues: 207.4819 Evaluate side-chains 274 residues out of total 3483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 215 time to evaluate : 1.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 131 SER Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 474 SER Chi-restraints excluded: chain A residue 487 LEU Chi-restraints excluded: chain A residue 624 VAL Chi-restraints excluded: chain A residue 735 THR Chi-restraints excluded: chain A residue 836 LEU Chi-restraints excluded: chain A residue 965 ILE Chi-restraints excluded: chain B residue 128 SER Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain C residue 207 VAL Chi-restraints excluded: chain C residue 234 ARG Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 272 MET Chi-restraints excluded: chain C residue 329 LEU Chi-restraints excluded: chain C residue 367 THR Chi-restraints excluded: chain C residue 419 MET Chi-restraints excluded: chain C residue 487 LEU Chi-restraints excluded: chain C residue 557 MET Chi-restraints excluded: chain C residue 612 LEU Chi-restraints excluded: chain C residue 632 ASN Chi-restraints excluded: chain C residue 641 THR Chi-restraints excluded: chain C residue 685 VAL Chi-restraints excluded: chain C residue 751 THR Chi-restraints excluded: chain C residue 836 LEU Chi-restraints excluded: chain C residue 891 VAL Chi-restraints excluded: chain C residue 903 SER Chi-restraints excluded: chain C residue 965 ILE Chi-restraints excluded: chain D residue 61 GLN Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain E residue 32 HIS Chi-restraints excluded: chain E residue 36 THR Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 129 ILE Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain G residue 153 LEU Chi-restraints excluded: chain G residue 326 MET Chi-restraints excluded: chain G residue 340 VAL Chi-restraints excluded: chain G residue 354 VAL Chi-restraints excluded: chain G residue 394 MET Chi-restraints excluded: chain G residue 433 LEU Chi-restraints excluded: chain G residue 472 THR Chi-restraints excluded: chain G residue 478 MET Chi-restraints excluded: chain G residue 509 VAL Chi-restraints excluded: chain G residue 513 LEU Chi-restraints excluded: chain G residue 549 VAL Chi-restraints excluded: chain H residue 37 THR Chi-restraints excluded: chain H residue 60 VAL Chi-restraints excluded: chain H residue 68 LEU Chi-restraints excluded: chain H residue 92 ASN Chi-restraints excluded: chain H residue 137 TYR Chi-restraints excluded: chain H residue 340 VAL Chi-restraints excluded: chain H residue 417 MET Chi-restraints excluded: chain H residue 499 THR Chi-restraints excluded: chain H residue 509 VAL Chi-restraints excluded: chain H residue 541 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 85 optimal weight: 5.9990 chunk 158 optimal weight: 5.9990 chunk 272 optimal weight: 20.0000 chunk 237 optimal weight: 0.7980 chunk 6 optimal weight: 1.9990 chunk 104 optimal weight: 10.0000 chunk 41 optimal weight: 0.9990 chunk 36 optimal weight: 0.2980 chunk 113 optimal weight: 0.4980 chunk 98 optimal weight: 0.6980 chunk 258 optimal weight: 0.6980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 179 ASN ** B 398 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 809 GLN F 51 HIS F 108 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.102115 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.065618 restraints weight = 68580.936| |-----------------------------------------------------------------------------| r_work (start): 0.3008 rms_B_bonded: 2.55 r_work: 0.2895 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2774 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.2774 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8940 moved from start: 0.2831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 33714 Z= 0.105 Angle : 0.575 16.092 45849 Z= 0.296 Chirality : 0.041 0.300 5028 Planarity : 0.003 0.071 5916 Dihedral : 5.253 57.162 5188 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.89 % Favored : 95.97 % Rotamer: Outliers : 1.52 % Allowed : 15.22 % Favored : 83.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.38 (0.13), residues: 4115 helix: 1.07 (0.18), residues: 866 sheet: 0.53 (0.14), residues: 1167 loop : -0.18 (0.14), residues: 2082 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 128 TYR 0.022 0.001 TYR E 74 PHE 0.013 0.001 PHE F 110 TRP 0.025 0.001 TRP H 274 HIS 0.015 0.001 HIS F 51 Details of bonding type rmsd/Z covalent geometry : bond 0.00223 / 0.10 (33685) covalent geometry : angle 0.57291 / 0.30 (45762) hydrogen bonds : bond 0.02894 / 1.97 ( 1463) hydrogen bonds : angle 4.60170 / 3.20 ( 4005) link_ALPHA1-6 : bond 0.00750 / 0.41 ( 29) link_ALPHA1-6 : angle 1.37315 / 0.91 ( 87) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8230 Ramachandran restraints generated. 4115 Oldfield, 0 Emsley, 4115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8230 Ramachandran restraints generated. 4115 Oldfield, 0 Emsley, 4115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 3483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 240 time to evaluate : 1.298 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 LYS cc_start: 0.8288 (mmtm) cc_final: 0.7948 (mmmm) REVERT: A 234 ARG cc_start: 0.9139 (mtp85) cc_final: 0.8856 (mtm-85) REVERT: A 401 GLN cc_start: 0.9222 (tp40) cc_final: 0.8794 (tp40) REVERT: A 518 ASP cc_start: 0.8792 (p0) cc_final: 0.8552 (p0) REVERT: A 957 PHE cc_start: 0.8547 (m-80) cc_final: 0.8284 (m-10) REVERT: B 194 MET cc_start: 0.8717 (ptt) cc_final: 0.8401 (ptp) REVERT: B 217 MET cc_start: 0.8444 (ttm) cc_final: 0.8006 (ttp) REVERT: B 246 MET cc_start: 0.7789 (tpp) cc_final: 0.7368 (mtt) REVERT: C 419 MET cc_start: 0.9034 (OUTLIER) cc_final: 0.7742 (mpp) REVERT: D 61 GLN cc_start: 0.9238 (OUTLIER) cc_final: 0.8718 (tm-30) REVERT: E 142 ARG cc_start: 0.7940 (mtm180) cc_final: 0.7722 (mpp80) REVERT: F 33 ASP cc_start: 0.8664 (t0) cc_final: 0.8373 (t0) REVERT: F 51 HIS cc_start: 0.8436 (OUTLIER) cc_final: 0.7851 (p-80) REVERT: F 70 ASN cc_start: 0.9231 (m-40) cc_final: 0.8985 (m-40) REVERT: F 103 LYS cc_start: 0.7768 (mmmm) cc_final: 0.7549 (mmmm) REVERT: F 108 ASN cc_start: 0.8536 (m110) cc_final: 0.8111 (m110) REVERT: F 122 LYS cc_start: 0.8918 (ttpp) cc_final: 0.8549 (tmtm) REVERT: F 136 MET cc_start: 0.8795 (mtm) cc_final: 0.8312 (ptp) REVERT: G 219 MET cc_start: 0.8847 (mmm) cc_final: 0.8491 (mmm) REVERT: G 326 MET cc_start: 0.8685 (OUTLIER) cc_final: 0.8411 (mpp) REVERT: G 433 LEU cc_start: 0.8284 (OUTLIER) cc_final: 0.7944 (mm) REVERT: G 457 TYR cc_start: 0.8889 (m-80) cc_final: 0.8548 (m-80) REVERT: G 463 TYR cc_start: 0.8640 (m-80) cc_final: 0.8285 (m-80) REVERT: H 92 ASN cc_start: 0.8094 (OUTLIER) cc_final: 0.7587 (t0) REVERT: H 156 MET cc_start: 0.9114 (mmm) cc_final: 0.8211 (mmm) REVERT: H 219 MET cc_start: 0.8707 (mmm) cc_final: 0.7615 (mmm) REVERT: H 394 MET cc_start: 0.8217 (mmm) cc_final: 0.7133 (mmm) outliers start: 53 outliers final: 34 residues processed: 276 average time/residue: 0.6313 time to fit residues: 213.3963 Evaluate side-chains 260 residues out of total 3483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 220 time to evaluate : 1.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 474 SER Chi-restraints excluded: chain A residue 624 VAL Chi-restraints excluded: chain A residue 836 LEU Chi-restraints excluded: chain B residue 128 SER Chi-restraints excluded: chain C residue 207 VAL Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 272 MET Chi-restraints excluded: chain C residue 329 LEU Chi-restraints excluded: chain C residue 367 THR Chi-restraints excluded: chain C residue 419 MET Chi-restraints excluded: chain C residue 487 LEU Chi-restraints excluded: chain C residue 557 MET Chi-restraints excluded: chain C residue 632 ASN Chi-restraints excluded: chain C residue 641 THR Chi-restraints excluded: chain C residue 891 VAL Chi-restraints excluded: chain C residue 965 ILE Chi-restraints excluded: chain D residue 61 GLN Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain E residue 32 HIS Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 129 ILE Chi-restraints excluded: chain F residue 50 ASN Chi-restraints excluded: chain F residue 51 HIS Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain G residue 326 MET Chi-restraints excluded: chain G residue 340 VAL Chi-restraints excluded: chain G residue 433 LEU Chi-restraints excluded: chain G residue 509 VAL Chi-restraints excluded: chain G residue 513 LEU Chi-restraints excluded: chain H residue 37 THR Chi-restraints excluded: chain H residue 60 VAL Chi-restraints excluded: chain H residue 68 LEU Chi-restraints excluded: chain H residue 92 ASN Chi-restraints excluded: chain H residue 137 TYR Chi-restraints excluded: chain H residue 340 VAL Chi-restraints excluded: chain H residue 509 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 170 optimal weight: 1.9990 chunk 162 optimal weight: 0.9980 chunk 98 optimal weight: 0.8980 chunk 189 optimal weight: 6.9990 chunk 208 optimal weight: 3.9990 chunk 397 optimal weight: 20.0000 chunk 142 optimal weight: 3.9990 chunk 163 optimal weight: 5.9990 chunk 229 optimal weight: 0.9980 chunk 29 optimal weight: 0.3980 chunk 2 optimal weight: 8.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 398 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 809 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.101769 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.065569 restraints weight = 68449.936| |-----------------------------------------------------------------------------| r_work (start): 0.3008 rms_B_bonded: 2.53 r_work: 0.2894 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2774 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2774 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8944 moved from start: 0.2884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 33714 Z= 0.119 Angle : 0.571 16.087 45849 Z= 0.296 Chirality : 0.042 0.294 5028 Planarity : 0.003 0.069 5916 Dihedral : 5.175 59.522 5186 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.84 % Favored : 96.01 % Rotamer: Outliers : 1.44 % Allowed : 15.73 % Favored : 82.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.40 (0.13), residues: 4115 helix: 1.10 (0.18), residues: 866 sheet: 0.56 (0.15), residues: 1144 loop : -0.18 (0.14), residues: 2105 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 142 TYR 0.026 0.001 TYR B 457 PHE 0.017 0.001 PHE F 110 TRP 0.025 0.001 TRP H 274 HIS 0.007 0.001 HIS F 51 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.12 (33685) covalent geometry : angle 0.56871 / 0.30 (45762) hydrogen bonds : bond 0.02904 / 1.98 ( 1463) hydrogen bonds : angle 4.56605 / 3.18 ( 4005) link_ALPHA1-6 : bond 0.00728 / 0.39 ( 29) link_ALPHA1-6 : angle 1.39116 / 0.92 ( 87) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12741.95 seconds wall clock time: 217 minutes 53.07 seconds (13073.07 seconds total)